antarna: antaRNA.py annotate

annotate antaRNA.py @ 2:cfe9e6771518 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty

author	rnateam
date	Wed, 13 May 2015 11:17:08 -0400
parents	fcf4719d3831
children

rev	line source
0 fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1 import numpy
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	2 import sys
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	3 import random
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	4 import subprocess
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	5 import re
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	6 import decimal
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	7 import math
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	8 import os
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	9 import shutil
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	10 import time
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	11 import types
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	12 import argparse
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	13 #from argparse import RawTextHelpFormatter
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	14
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	15 #############################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	16 # FUNCTIONS
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	17
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	18 def print2file(f, i, m):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	19 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	20 print content i to file f in mode m
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	21 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	22 line = str(i)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	23 if m == "a":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	24 call = "echo \"" + line + "\" >> " + f
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	25 elif m == "w":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	26 call = "echo \"" + line + "\" > " + f
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	27 os.system(call)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	28
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	29 # checking and correcting the alphabet of the constraint sequence
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	30 def checkSequenceConstraint(SC):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	31 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	32 Checks the Sequence constraint for illegal nucleotide characters
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	33 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	34 out = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	35 for c in SC:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	36 c = c.upper()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	37 if c not in "ACGURYSWKMBDHVN":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	38 # and c!= "R" and c != "Y" and c != "S" and c != "W" and c != "K" and c != "M" and c != "B" and c != "D" and c != "H" and c != "V":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	39 if c == "T":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	40 c = "U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	41 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	42 print "\tIllegal Character in the constraint sequence!"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	43 print "\tPlease use the IUPAC nomenclature for defining nucleotides in the constraint sequence!"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	44 print "\tA Adenine"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	45 print "\tC Cytosine"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	46 print "\tG Guanine"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	47 print "\tT/U Thymine/Uracil"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	48 print "\tR A or G"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	49 print "\tY C or T/U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	50 print "\tS G or C"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	51 print "\tW A or T/U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	52 print "\tK G or T/U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	53 print "\tM A or C"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	54 print "\tB C or G or T/U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	55 print "\tD A or G or T/U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	56 print "\tH A or C or T/U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	57 print "\tV A or C or G"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	58 print "\tN any base"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	59 exit(0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	60 out += c
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	61 return (1, out)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	62
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	63
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	64 def transform(seq):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	65 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	66 Transforms "U" to "T" for the processing is done on DNA alphabet
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	67 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	68 S = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	69 for s in seq:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	70 if s == "T":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	71 S += "U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	72 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	73 S += s
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	74 return S
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	75
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	76
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	77 def checkSimilarLength(s, SC):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	78 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	79 Compares sequence and structure constraint length
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	80 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	81 if len(s) == len(SC):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	82 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	83 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	84 return 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	85
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	86
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	87 def isStructure(s):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	88 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	89 Checks if the structure constraint only contains "(", ")", and "." and legal fuzzy structure constraint characters.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	90 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	91 returnvalue = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	92 for a in range(0,len(s)):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	93 if s[a] not in ".()[]{}<>":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	94 if s[a] not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	95 returnvalue = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	96 return returnvalue
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	97
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	98
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	99 def isBalanced(s):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	100 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	101 Check if the structure s is of a balanced nature
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	102 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	103
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	104 balance = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	105 for bracket in ["()", "[]", "{}", "<>"]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	106 counter = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	107 for a in xrange(len(s)):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	108 if s[a] in bracket[0]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	109 counter += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	110 elif s[a] in bracket[1]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	111 counter -= 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	112 if counter != 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	113 balance = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	114 return balance
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	115
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	116
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	117
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	118 def fulfillsHairpinRule(s):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	119 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	120 CHECKING FOR THE 3 nt LOOP INTERSPACE
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	121 for all kind of basepairs, even wihtin the pdeudoknots
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	122 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	123
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	124 fulfillsRules = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	125 for bracket in ["()", "[]", "{}", "<>"]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	126 last_opening_char = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	127 check = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	128 for a in xrange(len(s)):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	129 if s[a] == bracket[0]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	130 last_opening_char = a
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	131 check = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	132 elif s[a] == bracket[1] and check == 1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	133 check = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	134 if a - last_opening_char < 4:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	135 return 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	136 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	137
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	138
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	139 def isValidStructure(s):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	140 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	141 Checks, if the structure s is a valid structure
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	142 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	143
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	144 Structure = isStructure(s)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	145 Balanced = isBalanced(s)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	146 HairpinRule = fulfillsHairpinRule(s)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	147
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	148 if Structure == 1 and Balanced == 1 and HairpinRule == 1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	149 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	150 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	151 print Structure, Balanced, HairpinRule
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	152 return 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	153
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	154 def loadIUPACcompatibilities(IUPAC, useGU):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	155 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	156 Generating a hash containing all compatibilities of all IUPAC RNA NUCLEOTIDES
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	157 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	158 compatible = {}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	159 for nuc1 in IUPAC: # ITERATING OVER THE DIFFERENT GROUPS OF IUPAC CODE
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	160 sn1 = list(IUPAC[nuc1])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	161 for nuc2 in IUPAC: # ITERATING OVER THE DIFFERENT GROUPS OF IUPAC CODE
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	162 sn2 = list(IUPAC[nuc2])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	163 compatib = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	164 for c1 in sn1: # ITERATING OVER THE SINGLE NUCLEOTIDES WITHIN THE RESPECTIVE IUPAC CODE:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	165 for c2 in sn2: # ITERATING OVER THE SINGLE NUCLEOTIDES WITHIN THE RESPECTIVE IUPAC CODE:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	166 # CHECKING THEIR COMPATIBILITY
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	167 if useGU == True:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	168 if (c1 == "A" and c2 == "U") or (c1 == "U" and c2 == "A") or (c1 == "C" and c2 == "G") or (c1 == "G" and c2 == "C") or (c1 == "G" and c2 == "U") or (c1 == "U" and c2 == "G"):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	169 compatib = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	170 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	171 if (c1 == "A" and c2 == "U") or (c1 == "U" and c2 == "A") or (c1 == "C" and c2 == "G") or (c1 == "G" and c2 == "C"):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	172 compatib = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	173 compatible[nuc1 + "_" + nuc2] = compatib # SAVING THE RESPECTIVE GROUP COMPATIBILITY, REVERSE SAVING IS NOT REQUIRED, SINCE ITERATING OVER ALL AGAINST ALL
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	174 return compatible
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	175
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	176 def isCompatibleToSet(c1, c2, IUPAC_compatibles):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	177 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	178 Checks compatibility of c1 wihtin c2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	179 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	180 compatible = True
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	181 for setmember in c2:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	182 #print setmember
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	183 if isCompatible(c1, setmember, IUPAC_compatibles) == False:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	184 return False
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	185 return compatible
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	186
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	187
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	188 def isCompatible(c1, c2, IUPAC_compatibles):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	189 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	190 Checks compatibility between character c1 and c2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	191 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	192 if IUPAC_compatibles[c1 + "_" + c2] == 1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	193 return True
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	194 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	195 return False
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	196
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	197
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	198 def isStructureCompatible(lp1, lp2 ,bp):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	199 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	200 Checks, if the region within lp1 and lp2 is structurally balanced
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	201 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	202 x = lp1 + 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	203 while (x < lp2):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	204 if (bp[x] <= lp1 or bp[x] > lp2):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	205 return False
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	206 if x == bp[x]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	207 x += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	208 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	209 x = bp[x] + 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	210 return x == lp2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	211
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	212
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	213 def checkConstaintCompatibility(basepairstack, sequenceconstraint, IUPAC_compatibles):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	214 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	215 Checks if the constraints are compatible to each other
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	216 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	217 returnstring = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	218 compatible = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	219 for id1 in basepairstack: # key = (constraint , (pos, constraint)))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	220 constr1 = basepairstack[id1][0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	221 id2 = basepairstack[id1][1][0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	222 constr2 = basepairstack[id1][1][1]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	223
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	224 if id1 != id2 and not isCompatible(constr1, constr2, IUPAC_compatibles):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	225
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	226 compatible = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	227 returnstring += "nucleotide constraint " + str(constr1) + " at position " + str(id1) + " is not compatible with nucleotide constraint " + str(constr2) + " at position " + str(id2) + "\n"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	228 #if not isCompatible(basepairstack[basepair][0], basepairstack[basepair][1][1]):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	229
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	230 #compatible = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	231 #else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	232 #returnstring += "nucleotide constraint " + str(basepairstack[basepair][0]) + " at position " + str(basepair) + " is compatible with nucleotide constraint " + str(basepairstack[basepair][1][1]) + " at position " + str(basepairstack[basepair][1][0]) + "\n"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	233 return (compatible, returnstring)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	234
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	235
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	236 def getLP(BPSTACK):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	237 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	238 Retreives valid lonley base pairs from a base pair stack
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	239 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	240 #20 ('N', (>BLOCK<, 'N'))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	241
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	242 # geting single base pairs
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	243 stack = {}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	244 LP = {}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	245 if type(BPSTACK[random.choice(BPSTACK.keys())]) == types.TupleType:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	246 for i in BPSTACK.keys():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	247 #if str(BPSTACK[i][1][0]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	248 stack[i] = int(BPSTACK[i][1][0])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	249 #print i , BPSTACK[i][1][0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	250 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	251 for i in BPSTACK.keys():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	252 #if str(BPSTACK[i]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	253 stack[i] = BPSTACK[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	254
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	255 # removing redundant base pair indices
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	256 for i in stack.keys():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	257 if i >= stack[i]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	258 del stack[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	259
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	260 # actual checking for single lonley base pairs
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	261 for i in stack.keys():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	262 if not (i-1 in stack and stack[i-1] == stack[i] + 1) and not (i+1 in stack and stack[i+1] == stack[i] - 1):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	263 LP[i] = stack[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	264
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	265 ##actual removal of 2er lonley base pairs
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	266 for i in stack.keys():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	267 if not (i-1 in stack and stack[i-1] == stack[i] + 1) and (i+1 in stack and stack[i+1] == stack[i] - 1) and not (i+2 in stack and stack[i+2] == stack[i] - 2):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	268 LP[i] = stack[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	269 LP[i+1] = stack[i+1]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	270
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	271
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	272 #if type(BPSTACK[random.choice(BPSTACK.keys())]) == types.TupleType:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	273 #for i in BPSTACK.keys():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	274
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	275 ##if str(BPSTACK[i][1][0]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	276 #stack[i] = int(BPSTACK[i][1][0])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	277 ##print i , BPSTACK[i][1][0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	278 #else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	279 #for i in BPSTACK.keys():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	280 ##if str(BPSTACK[i]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	281 #stack[i] = BPSTACK[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	282
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	283 #for i in stack.keys():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	284 #if i >= stack[i]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	285 #del stack[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	286
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	287
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	288
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	289 return LP
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	290
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	291
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	292 def getBPStack(s, seq):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	293 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	294 Returns a dictionary of the corresponding basepairs of the structure s and the sequence constraint seq.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	295 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	296 tmp_stack = {"()":[], "{}":[], "[]":[], "<>":[]}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	297 bpstack = {}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	298 for i in xrange(len(s)):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	299
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	300 # REGULAR SECONDARY STRUCTURE DETECTION
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	301 if s[i] in "(){}[]<>":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	302
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	303 no = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	304 ### opening
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	305 if s[i] in "([{<":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	306 if s[i] == "(":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	307 tmp_stack["()"].append((i, seq[i]))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	308 elif s[i] == "[":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	309 tmp_stack["[]"].append((i, seq[i]))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	310 elif s[i] == "{":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	311 tmp_stack["{}"].append((i, seq[i]))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	312 elif s[i] == "<":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	313 tmp_stack["<>"].append((i, seq[i]))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	314
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	315 #closing
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	316 elif s[i] in ")]}>":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	317 if s[i] == ")":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	318 no, constr = tmp_stack["()"].pop()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	319 elif s[i] == "]":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	320 no, constr = tmp_stack["[]"].pop()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	321 elif s[i] == "}":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	322 no, constr = tmp_stack["{}"].pop()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	323 elif s[i] == ">":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	324 no, constr = tmp_stack["<>"].pop()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	325 bpstack[no] = (constr, (i, seq[i]))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	326 bpstack[i] = (seq[i] ,(no, constr))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	327
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	328 elif s[i] == ".":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	329 bpstack[i] = (seq[i], (i, seq[i]))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	330 elif s[i] in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	331 bpstack[i] = (seq[i], (i, seq[i]))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	332
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	333 return (bpstack, getLP(bpstack))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	334
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	335
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	336 def getbpStack(s):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	337 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	338 Returns a dictionary of the corresponding basepairs of the structure s and the sequence constraint seq.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	339 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	340 tmp_stack = {"()":[], "{}":[], "[]":[], "<>":[]}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	341 bpstack = {}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	342
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	343 for i in xrange(len(s)):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	344 if s[i] in "(){}[]<>":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	345
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	346 no = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	347 ### opening
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	348 if s[i] in "([{<":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	349 if s[i] == "(":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	350 tmp_stack["()"].append(i)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	351 elif s[i] == "[":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	352 tmp_stack["[]"].append(i)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	353 elif s[i] == "{":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	354 tmp_stack["{}"].append(i)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	355 elif s[i] == "<":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	356 tmp_stack["<>"].append(i)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	357
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	358 #closing
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	359 elif s[i] in ")]}>":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	360 if s[i] == ")":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	361 no = tmp_stack["()"].pop()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	362 elif s[i] == "]":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	363 no = tmp_stack["[]"].pop()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	364 elif s[i] == "}":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	365 no = tmp_stack["{}"].pop()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	366 elif s[i] == ">":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	367 no = tmp_stack["<>"].pop()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	368 bpstack[no] = i # save basepair in the format {opening base id (opening seq constr,(closing base id, closing seq constr))}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	369 bpstack[i] = no # save basepair in the format {closing base id (closing seq constr,(opening base id, opening seq constr))}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	370
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	371 elif s[i] == ".": # no structural constaint given: produce entry, which references itself as a base pair partner....
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	372 bpstack[i] = i
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	373
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	374 elif s[i] in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	375 bpstack[i] = i
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	376
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	377 #elif s[i] in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	378 ## per position, assigned to a certain block, the target nucleotide, with whcih it should interact is marked with the specific
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	379 ## block character
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	380 #bpstack[i] = s[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	381
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	382 return (bpstack, getLP(bpstack))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	383
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	384 def maprange( a, b, s):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	385 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	386 Mapping function
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	387 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	388 (a1, a2), (b1, b2) = a, b
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	389 return b1 + ((s - a1) * (b2 - b1) / (a2 - a1))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	390
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	391
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	392 def applyGCcontributionPathAdjustment(pathlength, tmpGC, nt):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	393 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	394 GC path length contribution calculation.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	395 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	396 GCadjustment = 1.5
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	397 minimum = 0.5
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	398 upper = GCadjustment
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	399 lower = minimum
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	400
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	401 if nt == "A" or nt == "U":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	402 pathlength = pathlength * maprange( (0, 1) , (lower, upper), tmpGC)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	403
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	404 if nt == "G" or nt == "C":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	405 #pathlength = pathlength * (float(1-tmpGC))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	406 pathlength = pathlength * maprange( (1, 0) , (lower, upper), tmpGC)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	407 return pathlength
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	408
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	409 def getConstraint(TE, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	410 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	411 Dependend on the situation in the constraint an the respective path section, setting wether a specific constraint can be given or not (for that path section)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	412 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	413 # TE :: transition element / path section under dispute
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	414 # id1 :: id of the position of the caharacter to which the transition is leading to
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	415 # id2 :: id of the position of the character, which is listed in the BPinformation, it can be id1 as well, when no bp is present
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	416 # val :: BPstack information of the specific position
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	417 # constr1 :: constraining character of pos id1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	418 # constr2 :: constraining character of pos id2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	419
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	420 id1 = int(TE.split(".")[0])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	421 val = BPstack[id1] # check out the value of the destination character in the basepair/constraint stack
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	422 constr1 = val[0] # getting the constraint character of position id1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	423 id2 = int(val[1][0]) # getting position id2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	424 constr2 = val[1][1] # getting the sequence constraint for position id2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	425 targetNucleotide = TE.split(".")[1][-1:] # where the edge is leading to
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	426
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	427 c1 = set(IUPAC[constr1]) # getting all explicit symbols of c1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	428 c2 = set(IUPAC_reverseComplements[constr2]) # getting the reverse complement explicit symbols of c2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	429
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	430 if targetNucleotide in c1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	431 if id1 == id2:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	432 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	433 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	434 if targetNucleotide in c2:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	435 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	436 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	437 return 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	438 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	439 return 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	440
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	441 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	442 def getConstraint(TE, BPstack):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	443 # TE :: transition element / path section
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	444 # id1 :: id of the position of the caharacter to which the transition is leading to
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	445 # id2 :: id of the position of the character, which is listed in the BPinformation, it can be id1 as well, when no bp is present
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	446 # val :: BPstack information of the specific position
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	447 # constr1 :: constraining character of pos id1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	448 # constr2 :: constraining character of pos id2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	449
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	450 ### BPstack [id1] = (constr1, (id2, constr2))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	451
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	452 id1 = TE.split(".")[0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	453 #print id1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	454 #id1 = TE.find(TE.strip("_")) # strip the path section and getting the position of the section
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	455 #if len(TE.strip("_")) == 2: # check if the path section is from an internal and not an initial transition
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	456 #id1 += 1 # increase position id1 by 1, since the last character of the section is the destination character
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	457 val = BPstack[int(id1)] # check out the value of the destination character in the basepair/constraint stack
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	458 constr1 = val[0] # getting the constraint character of position id1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	459 id2 = val[1][0] # getting position id2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	460 constr2 = val[1][1] # getting the sequence constraint for position id2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	461 #print TE, id1, constr1, id2, constr2,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	462
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	463 #TE.split(".")[1][-1:]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	464 if id1 == id2: # both ids were the same with either character, sequential or no sequential constraint -> no basepair constraint
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	465 if constr1 == TE.split(".")[1][-1:] and constr2 == TE.split(".")[1][-1:]: # case if the single base constraints on position id1 == id2 are the same as the destination character on id1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	466 #print 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	467 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	468 elif constr1 == constr2 == "N": # case if the single base constraints on position id1 == id2 has no constraint
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	469 #print 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	470 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	471 else: # single base sequence constraints differ
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	472 #print 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	473 return 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	474
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	475 elif id1 != id2: # showing differentq ids, indicating a bp, (basepair structural constraint)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	476 if constr1 == "N" and constr2 == "N": # no sequence constraint
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	477 #print 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	478 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	479 if constr1 == "N" and constr2 != "N": # c1 has no constraint, c2 has character constraint (sequence constraint of closing bases)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	480 if TE.split(".")[1][-1:] == complementBase(constr2): # the current path section destination base is equal to the complement base of the mentioned sequence constraint in constr2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	481 #print 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	482 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	483 else: # case if the current path section destination base is not equeal to the mentioned complement sequence constraint in constr2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	484 #print 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	485 return 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	486 if constr1 != "N" and constr2 == "N": # c1 has character constraint, c2 has no character constraint (sequence constraint in the opening base)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	487 if TE.split(".")[1][-1:] == constr1: # the current path section destination base is as constrained with constr1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	488 #print 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	489 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	490 else: # the current path section destination base is not as constrained in constr1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	491 #print 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	492 return 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	493 if constr1 != "N" and constr2 != "N": # both positions have sequential constraint
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	494 if TE.split(".")[1][-1:] == constr1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	495 #print 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	496 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	497 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	498 #print 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	499 return 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	500 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	501
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	502 def applyTerrainModification(terrain, s, tmpGC, SC, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	503 #nucleotides = {'A': 0, 'C': 1,'G': 2,'T': 3}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	504
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	505 dels = []
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	506 for terrainelement in sorted(terrain):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	507 pheromone, pathlength = terrain[terrainelement]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	508 pheromone = getConstraint(terrainelement, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	509 pathlength = getConstraint(terrainelement, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	510 pathlength = applyGCcontributionPathAdjustment(pathlength, tmpGC,terrainelement.split(".")[1][-1:])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	511 if pheromone * pathlength == 0: dels.append(terrainelement)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	512 terrain[terrainelement] = (pheromone, pathlength,[])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	513 further_dels = {}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	514 for terrainelement in sorted(dels):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	515 pos, nucs = terrainelement.split(".")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	516 if int(pos) < len(s)-1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	517 to_nt = nucs[-1:]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	518 successor_pos = int(pos) + 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	519 for i in ["A", "C", "G", "U"]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	520 del_element = str(successor_pos) + "." + to_nt + i
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	521 further_dels[del_element] = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	522 further_dels[terrainelement] = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	523 # deleting the inbound and outbound edges, which are forbidden
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	524 for terrainelement in further_dels:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	525 del terrain[terrainelement]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	526 # allocate the appropriate children of edges
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	527 for terrainelement in terrain:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	528 pheromone, pathlength, children = terrain[terrainelement]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	529 pos, nucs = terrainelement.split(".")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	530 if int(pos) < len(s):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	531 to_nt = nucs[-1:]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	532 successor_pos = int(pos) + 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	533 for i in ["A", "C", "G", "U"]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	534 if str(successor_pos) + "." + to_nt + i in terrain:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	535 children.append(str(successor_pos) + "." + to_nt + i)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	536 terrain[terrainelement] = (pheromone, pathlength,children)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	537 starts = []
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	538 for i in ["A", "C", "G", "U"]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	539 if str(0) + "." + i in terrain:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	540 starts.append(str(0) + "." + i)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	541 terrain["00.XY"] = (1, 1, starts)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	542 return (terrain, BPstack)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	543
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	544
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	545 def initTerrain(s): # THE CLASSIC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	546 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	547 Initialization of the terrain with graph like terrain... vertices are modeled implicitly
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	548 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	549 nt = ["A","C","G","U"]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	550 nt2 = ["AA","AC","AG","AU","CA","CC","CG","CU","GA","GC","GG","GU","UA","UC","UG","UU"] # Allowed dinucleotides
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	551 e = {}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	552 pathlength = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	553 pheromone = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	554 for p in xrange(len(s)):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	555 if p == 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	556 for i in nt:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	557 e["%s.%s"%(p,i)] = (pheromone, pathlength)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	558 elif p > 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	559 for n in nt2:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	560 e["%s.%s"%(p,n)] = (pheromone, pathlength)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	561 return e
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	562
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	563
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	564
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	565 def complementBase(c):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	566 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	567 Returns the complement RNA character of c (without GU base pairs)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	568 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	569 retChar = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	570 if c == "A" :
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	571 retChar = "U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	572 elif c == "U":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	573 retChar = "A"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	574 elif c == "C":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	575 retChar = "G"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	576 elif c == "G":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	577 retChar = "C"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	578 return retChar
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	579
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	580 def printTerrain(terrain):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	581 #print sorted(terrain.keys())
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	582 tmp_i = "0"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	583 tmp_c = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	584 terrain = terrain[0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	585
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	586 for a, i in enumerate(sorted(terrain.keys())):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	587 #print a
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	588 if i.split(".")[0] != tmp_i:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	589 print "\nElements:", tmp_c,"\n#########################\n", i, terrain[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	590
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	591 tmp_c = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	592 tmp_i = i.split(".")[0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	593 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	594 print i, terrain[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	595 tmp_c += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	596
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	597 print "\nElements:", tmp_c
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	598 print "#########################"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	599 print len(terrain)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	600
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	601 def pickStep(tmp_steps, summe):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	602 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	603 Selects a step within the terrain
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	604 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	605 if len(tmp_steps) == 1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	606 return tmp_steps[0][1] # returning the nucleotide of the only present step
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	607 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	608 rand = random.random() # draw random number
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	609 mainval = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	610 for choice in xrange(len(tmp_steps)):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	611 val, label = tmp_steps[choice]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	612 mainval += val/float(summe)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	613 if mainval > rand: # as soon, as the mainval gets larger than the random value the assignment is done
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	614 return label
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	615
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	616 def getPath(s, tmp_terrain, tmp_BPstack, alpha, beta, IUPAC, IUPAC_reverseComplements):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	617 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	618 Performs a walk through the terrain and assembles a sequence, while respecting the structure constraint and IUPAC base complementarity
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	619 of the base pairs GU, GC and AT
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	620 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	621 nt = ["A","C","G","U"]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	622 prev_edge = "00.XY"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	623 sequence = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	624 while len(sequence) < len(s):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	625 coming_from = sequence[-1:]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	626 summe = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	627 steps = []
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	628 i = len(sequence)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	629 allowed_nt = "ACGU"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	630 # base pair closing case check, with subsequent delivery of a reduced allowed nt set
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	631
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	632 if i > tmp_BPstack[i][1][0]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	633 jump = tmp_BPstack[i][1][0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	634 nuc_at_jump = sequence[jump]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	635 allowed_nt = IUPAC_reverseComplements[nuc_at_jump]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	636
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	637 #allowed_nt = complementBase(nuc_at_jump)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	638
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	639 # Checking for every possible nt if it is suitable for the selection procedure
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	640 for edge in tmp_terrain[prev_edge][-1]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	641
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	642 if edge[-1:] in allowed_nt:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	643 pheromone, PL , children = tmp_terrain[edge]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	644 #if PL > 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	645 value = ((float(pheromone * alpha)) + ((1/float(PL)) * beta))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	646 summe += value
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	647 steps.append((value, edge))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	648 prev_edge = pickStep(steps, summe)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	649 sequence += prev_edge[-1:]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	650
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	651 return sequence
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	652
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	653
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	654 ###
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	655 # STRUCTURE PREDICTORS
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	656 ###
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	657 def getPKStructure(sequence, temperature, mode = "A"):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	658 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	659 Initialization pKiss mfe pseudoknot prediction
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	660 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	661 p2p = "pKiss"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	662 #p2p = "/usr/local/pkiss/2014-03-17/bin/pKiss_mfe"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	663 strategy = "--strategy "
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	664 t = "--temperature " + str(temperature)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	665
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	666 if mode == "A": strategy += "A"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	667 elif mode == "B": strategy += "B"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	668 elif mode == "C": strategy += "C"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	669 elif mode == "D": strategy += "D"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	670 elif mode == "P": strategy += "P"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	671
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	672 p = subprocess.Popen( ([p2p, "--mode mfe", strategy, t]),
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	673 #shell = True,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	674 stdin = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	675 stdout = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	676 stderr = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	677 close_fds = True)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	678 #print p.stderr.readline()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	679
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	680 p.stdin.write(sequence+'\n')
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	681 pks = p.communicate()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	682 structure = "".join(pks[0].split("\n")[2].split(" ")[-1:])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	683 return structure
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	684
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	685 def init_RNAfold(version, temperature, paramFile = ""):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	686 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	687 Initialization RNAfold listener
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	688 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	689 p2p = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	690 t = "-T " + str(temperature)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	691 P = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	692 if paramFile != "":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	693 P = "-P " + paramFile
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	694 if version == 185:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	695 p2p = "/home/rk/Software/ViennaRNA/ViennaRNA-1.8.5/Progs/RNAfold"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	696 p = subprocess.Popen( ([p2p, '--noPS', '-d 2', t, P]),
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	697 shell = True,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	698 stdin = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	699 stdout = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	700 stderr = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	701 close_fds = True)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	702 return p
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	703 elif version == 213:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	704 p2p = "RNAfold"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	705 p = subprocess.Popen( ([p2p, '--noPS', '-d 2', t, P]),
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	706 #shell = True,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	707 stdin = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	708 stdout = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	709 stderr = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	710 close_fds = True)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	711 return p
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	712 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	713 exit(0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	714
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	715 def consult_RNAfold(seq, p):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	716 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	717 Consults RNAfold listener
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	718 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	719 p.stdin.write(seq+'\n')
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	720 out = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	721 for i in xrange(2):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	722 out += p.stdout.readline()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	723 return out
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	724
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	725
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	726 def getRNAfoldStructure(struct2, process1):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	727 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	728 Retrieves folded structure of a RNAfold call
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	729 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	730
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	731 RNAfold_pattern = re.compile('.+\n([.()]+)\s.+')
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	732 #RNAdist_pattern = re.compile('.*\s([\d]+)')
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	733 RNAfold_match = RNAfold_pattern.match(consult_RNAfold(struct2, process1))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	734 current_structure = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	735 #if RNAfold_match:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	736 return RNAfold_match.group(1)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	737
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	738
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	739 def init_RNAdistance():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	740 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	741 Initialization of RNAdistance listener
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	742 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	743 #p2p = "/home/rk/Software/ViennaRNA/ViennaRNA-1.8.5/Progs/RNAdistance"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	744 p2p = "RNAdistance"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	745 p = subprocess.Popen( ([p2p]),
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	746 #shell = True,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	747 stdin = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	748 stdout = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	749 stderr = subprocess.PIPE,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	750 close_fds = True)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	751 return p
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	752
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	753
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	754 def consult_RNAdistance(s1, s2, p):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	755 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	756 Consulting the RNAdistance listener
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	757 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	758 p.stdin.write(s1+'\n')
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	759 p.stdin.write(s2+'\n')
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	760 out = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	761 out_tmp = p.stdout.readline().strip()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	762 if out_tmp != "":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	763 out += out_tmp
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	764 return out
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	765
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	766 def getInducingSequencePositions(Cseq, degreeOfSequenceInducement):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	767 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	768 Delimiting the degree of structure inducement by the supplied sequence constraint.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	769 0 : no sequence induced structure constraint
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	770 1 : "ACGT" induce structure (explicit nucleotide structure inducement level)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	771 2 : "MWKSYR" and "ACGT" (explicit and double instances)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	772 3 : "BDHV" , "MWKSYR" and "ACGT" (explicit, double, and triple instances)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	773 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	774 setOfNucleotides = "" # resembling the "0"-case
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	775 if degreeOfSequenceInducement == 1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	776 setOfNucleotides = "ACGU"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	777 elif degreeOfSequenceInducement == 2:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	778 setOfNucleotides = "ACGUMWKSYR"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	779 elif degreeOfSequenceInducement == 3:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	780 setOfNucleotides = "ACGUMWKSYRBDHV"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	781 #elif degreeOfSequenceInducement == 4:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	782 #setOfNucleotides = "ACGTMWKSYRBDHVN"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	783
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	784 tmpSeq = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	785 listset = setOfNucleotides
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	786 for pos in Cseq:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	787 if pos not in listset:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	788 tmpSeq += "N"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	789 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	790 tmpSeq += pos
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	791
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	792 return setOfNucleotides, tmpSeq
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	793
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	794
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	795 def getBPDifferenceDistance(stack1, stack2):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	796 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	797 Based on the not identical amount of base pairs within both structure stacks
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	798 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	799 d = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	800 for i in stack1.keys():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	801 # check base pairs in stack 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	802 if i < stack1[i] and stack1[i] != stack2[i]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	803 d += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	804 # check base pairs in stack 2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	805 for i in stack2.keys():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	806 if i < stack2[i] and stack1[i] != stack2[i]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	807 d += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	808 return d
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	809
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	810
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	811 def getStructuralDistance(target_structure, Cseq, path, RNAfold, verbose, LP, BP, RNAfold_pattern, IUPAC_compatibles, degreeOfSequenceInducement, pseudoknots, strategy):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	812 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	813 Calculator for Structural Distance
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	814 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	815 # fold the current solution's sequence to obtain the structure
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	816
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	817 current_structure = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	818
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	819 if pseudoknots:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	820 current_structure = getPKStructure(path,strategy)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	821 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	822 RNAfold_match = RNAfold_pattern.match(consult_RNAfold(path, RNAfold))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	823 current_structure = RNAfold_match.group(1)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	824
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	825 # generate the current structure's base-pair stack
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	826 bp = getbpStack(current_structure)[0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	827 # add case-dependend structural constraints in case of lonley basepairs formation
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	828 tmp_target_structure_bp = getbpStack(target_structure)[0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	829
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	830 for lp in LP:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	831 if bp[lp] == LP[lp]: # if the base pair is within the current solution structure, re-add the basepair into the constraint structure.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	832 #tmp_target_structure[lp] = "("
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	833 #tmp_target_structure[LP[lp]] = ")"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	834 tmp_target_structure_bp[lp] = LP[lp]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	835 tmp_target_structure_bp[LP[lp]] = lp
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	836
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	837 # REMOVE BLOCK CONSTRAINT AND SUBSTITUTE IT WITH SINGLE STRAND INFORMATION repsective with brackets, if allowed base pairs occure
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	838 # check for all allowed implicit constraint block declarators
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	839 for c in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	840 occurances = []
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	841 for m in re.finditer(c, target_structure): # search for a declarator in the requested structure
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	842 occurances.append(m.start()) # save the corresponding index
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	843
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	844 # transform declarator into single stranded request
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	845 for i in occurances:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	846 #tmp_target_structure[i] = "."
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	847 tmp_target_structure_bp[i] = i
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	848 # infer a base pair within the block declarated positions, if the current structure provides it.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	849 for i in occurances:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	850 for j in occurances:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	851 if i < j:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	852 if bp[i] == j:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	853 #tmp_target_structure[i] = "("
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	854 #tmp_target_structure[bp[i]] = ")"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	855
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	856 tmp_target_structure_bp[i] = bp[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	857 tmp_target_structure_bp[bp[i]] = i
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	858
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	859 # CHECK FOR SEQUENCE CONSTRAINT WHICH INDUCES STRUCTURE CONSTRAINT IN THE MOMENTARY SITUATION
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	860 #print "Checking Cseq influence and it's induced basepairs..."
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	861 IUPACinducers, tmp_Cseq = getInducingSequencePositions(Cseq, degreeOfSequenceInducement)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	862 if len(Cseq.strip("N")) > 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	863 #print "Processing Cseq influence"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	864 # Iterate over all positions within the Base Pair stack
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	865 for i in BP: # Check for each base index i
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	866
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	867 if i < bp[i]: # if the current index is samller that the affiliated in the basepair stack of the current solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	868
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	869 bp_j = bp[i] # Actual j index of the current solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	870 BP_j = BP[i][1][0] # j index of the requested structure
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	871 if (i != bp_j and i == BP_j and BP[i][0] in IUPACinducers ): # if i pairs with some other base in the current structure, and i is requested single stranded and the Sequence constraint is allowed to induce...
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	872 if (BP[bp_j][1][0] == bp_j and BP[bp_j][0] in IUPACinducers):# If position j is requested singlestranded and position j nucleotide can induce base pairs
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	873 #if isCompatible(bp[i][0], bp[i][1][1], IUPAC_compatibles): # If both nucleotides, i and j are actually compatible
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	874 #tmp_target_structure[i] = "("
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	875 #tmp_target_structure[bp_j] = ")"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	876
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	877 tmp_target_structure_bp[i] = bp[i]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	878 tmp_target_structure_bp[bp_j] = i
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	879
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	880 #tts = "".join(tmp_target_structure)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	881 dsreg = getBPDifferenceDistance(tmp_target_structure_bp, bp)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	882
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	883 # CHECK FOR ALL DETERMINED LONELY BASE PAIRS (i<j), if they are formed
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	884 failLP = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	885 for lp in LP:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	886
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	887 if bp[lp] != LP[lp]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	888
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	889 isComp = isCompatible(path[lp],path[LP[lp]], IUPAC_compatibles)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	890 isStru = isStructureCompatible(lp, LP[lp] ,bp)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	891 if not ( isStru and isStru ): # check if the bases at the specific positions are compatible and check if the
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	892 # basepair can be formed according to pseudoknot free restriction. If one fails, a penalty distance is raised for that base pair
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	893 failLP += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	894
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	895 #print dsreg, failLP, float(len(tmp_target_structure_bp))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	896 dsLP = float(failLP)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	897
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	898 return (dsreg + dsLP) /float(len(tmp_target_structure_bp))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	899
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	900
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	901 def getGC(sequence):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	902 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	903 Calculate GC content of a sequence
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	904 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	905 GC = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	906 for nt in sequence:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	907 if nt == "G" or nt == "C":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	908 GC = GC + 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	909 GC = GC/float(len(sequence))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	910 return GC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	911
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	912
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	913 def getGCDistance(tGC, gc2, L):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	914 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	915 Calculate the pseudo GC content distance
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	916 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	917 nt_coeff = L * tGC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	918 pc_nt = (1/float(L))*100
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	919 #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	920 d = gc2 - tGC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	921 d = d * 100
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	922
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	923 f = math.floor(nt_coeff)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	924 c = math.ceil(nt_coeff)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	925
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	926 if d < 0: #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	927 #print "case x",(abs(nt_coeff - f)), pc_nt, (abs(nt_coeff - f)) * pc_nt,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	928 d = d + (abs(nt_coeff - f)) * pc_nt
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	929 elif d > 0: # case y
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	930 #print "case y", abs(nt_coeff - c), pc_nt, abs(nt_coeff - c) * pc_nt,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	931 d = d - abs(nt_coeff - c) * pc_nt
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	932 elif d == 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	933 pass
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	934
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	935 d = round(d, 7)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	936 #d = max(0, abs(d)- ( max ( abs( math.ceil(nt_coeff)-(nt_coeff)) , abs(math.floor(nt_coeff)-(nt_coeff)) )/L)*100 )
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	937 return abs(d)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	938
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	939
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	940 def getSequenceEditDistance(SC, path):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	941 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	942 Calculate sequence edit distance of a solution to the constraint
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	943 """#
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	944 IUPAC = {"A":"A", "C":"C", "G":"G", "U":"U", "R":"AG", "Y":"CU", "S":"GC", "W":"AU","K":"GU", "M":"AC", "B":"CGU", "D":"AGU", "H":"ACU", "V":"ACG", "N":"ACGU"}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	945 edit = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	946 for i in xrange(len(SC)):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	947 if path[i] not in IUPAC[SC[i]]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	948 edit += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	949 return edit/float(len(path))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	950
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	951
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	952
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	953 def getTransitions(p):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	954 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	955 Retreive transitions of a specific path/sequence
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	956 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	957 transitions = []
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	958 for pos in xrange(len(p)):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	959 if pos == 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	960 transitions.append(str(pos) + "." + p[pos])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	961
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	962 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	963 insert = p[pos-1] + p[pos]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	964 transitions.append(str(pos) + "." + insert)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	965
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	966 return transitions
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	967
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	968
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	969 def evaporate(t, er):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	970 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	971 Evaporate the terrain's pheromone trails
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	972 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	973 terr, BP = t
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	974 c = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	975 for key in terr:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	976 p,l,c = terr[key]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	977 p *= (1-er)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	978 terr[key] = (p, l, c)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	979
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	980
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	981 def updateValue(distance, correction_term, omega):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	982 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	983 Retrieves a distance dependend pheromone value
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	984 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	985 if correction_term == 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	986 return 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	987 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	988 if distance == 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	989 return omega * correction_term
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	990 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	991 return (1/float(distance)) * correction_term
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	992
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	993
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	994 def trailBlaze(p, c_s, s, ds, dgc, dseq, dn, t, correction_terms, BPstack, verbose):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	995 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	996 Pheromone Update function accorinding to the quality of the solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	997 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	998 terr, BP = t
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	999 bpstack, LP = getbpStack(c_s)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1001 struct_correction_term , GC_correction_term, seq_correction_term = correction_terms
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1002 omega = 2.23
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1003
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1004 bs = updateValue(ds, struct_correction_term, omega)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1005 bGC = updateValue(dgc, GC_correction_term, omega)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1006 if dseq != "n.a.":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1007 bSeq = updateValue(dseq, seq_correction_term, omega)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1008 d = bs + bGC + bSeq
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1009 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1010 d = bs + bGC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1011 transitions = getTransitions(p)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1012
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1013 for trans in xrange(len(transitions)): # for each transition in the path
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1014 id1 = int(transitions[trans].split(".")[0])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1015 tar_id2 = int(BPstack[id1][1][0]) # getting requested position id2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1016 curr_id2 = int(bpstack[id1]) # getting the current situation
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1017 multiplicator = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1018 if tar_id2 == curr_id2 and id1 != tar_id2 and id1 != curr_id2: # case of a base pair, having both brackets on the correct position
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1019 multiplicator = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1020 elif tar_id2 == curr_id2 and id1 == tar_id2 and id1 == curr_id2: # case of a single stranded base in both structures
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1021 multiplicator = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1022 p, l, c = terr[transitions[trans]] # getting the pheromone and the length value of the single path transition
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1023 p += d * multiplicator
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1024 terr[transitions[trans]] = (p, l, c) # updating the values wihtin the terrain's
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1025 t = (terr, BP)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1026
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1027
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1028 def updateTerrain(p, c_s, s, ds, dgc, dseq, dn, t, er, correction_terms, BPstack, verbose, ant_count):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1029 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1030 General updating function
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1031 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1032 evaporate(t,er)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1033 trailBlaze(p, c_s, s, ds, dgc, dseq, dn, t, correction_terms, BPstack, verbose)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1034
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1035
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1036 def getUsedTime(start_time):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1037 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1038 Return the used time between -start time- and now.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1039 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1040 end_time = time.time()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1041 return end_time - start_time
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1042
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1043
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1044 def good2Go(SC, L, CC, STR):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1045 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1046 Check, if all input is correct and runnable
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1047 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1048 if (SC == 1 and L == 1 and CC == 1 and STR == 1):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1049 return True
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1050 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1051 print SC,L,CC,STR
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1052 return False
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1053
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1054
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1055 def getPathFromSelection( aps, s, terrain, alpha, beta, RNAfold, RNAfold_pattern, GC, SC, LP, verbose, IUPAC_compatibles, degreeOfSequenceInducement, IUPAC_reverseComplements, IUPAC, pseudoknots, strategy):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1056 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1057 Returns the winning path from a selection of pathes...
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1058 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1059 terr, BPs = terrain
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1060 win_path = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1061 for i in xrange(aps):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1062 # Generate Sequence
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1063 path = getPath(s, terr, BPs, alpha, beta, IUPAC, IUPAC_reverseComplements)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1064 # Measure sequence features and transform them into singular distances
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1065 distance_structural = float(getStructuralDistance(s, SC , path, RNAfold, verbose, LP, BPs, RNAfold_pattern, IUPAC_compatibles, degreeOfSequenceInducement, pseudoknots, strategy))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1066 distance_GC = float(getGCDistance(GC,getGC(path), len(path)))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1067 distance_seq = float(getSequenceEditDistance(SC, path))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1068 # Calculate Distance Score
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1069 D = distance_structural + distance_GC + distance_seq
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1070
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1071 # SELECT THE BEST-OUT-OF-k-SOLUTIONS according to distance score
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1072 if i == 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1073 win_path = (path, D, distance_structural, distance_GC, distance_seq)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1074 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1075 if D < win_path[1]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1076 win_path = (path, D, distance_structural, distance_GC, distance_seq)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1077 return win_path
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1078
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1079
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1080 def substr(x, string, subst):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1081 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1082 Classical substring function
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1083 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1084 s1 = string[:x-1]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1085
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1086 s2 = string[x-1:x]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1087 s3 = string[x:]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1088 #s2 = s[x+len(string)-x-1:]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1089
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1090 return s1 + subst + s3
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1091
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1092
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1093 def inConvergenceCorridor(d_struct, d_gc, BS_d_struct, BS_d_gc):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1094 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1095 Check if a solutions qualities are within the convergence corridor
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1096 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1097 struct_var = ((BS_d_struct/float(4)) + 3 ) * 4
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1098 gc_var = (BS_d_gc + 1/float(100) * 5) + BS_d_gc + 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1099
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1100 if d_struct <= struct_var and d_gc <= gc_var:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1101 return True
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1102 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1103 return False
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1104
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1105 def getGCSamplingValue(GC, tGCmax, tGCvar):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1106 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1107 Returns a suitable GC value, dependend on the user input: Either returning the single GC value,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1108 which the user entered, or a smpled GC value
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1109 from a designated distribution in it's interavals
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1110 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1111 returnval = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1112 if tGCmax == -1.0 and tGCvar == -1.0: # regular plain tGC value as requested
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1113 return GC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1114 elif tGCmax != -1.0 and tGCvar == -1.0: # uniform distribution tGC value sampling
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1115 if GC < tGCmax:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1116 tmp_GC = tGCmax
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1117 tGCmax = GC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1118 GC = tmp_GC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1119 while returnval <= 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1120 returnval = float(numpy.random.uniform(low=GC, high=tGCmax, size=1))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1121 return returnval
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1122 elif tGCmax == -1.0 and tGCvar != -1.0: # normal distribution tGC value sampling
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1123 while returnval <= 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1124 returnval = float(numpy.random.normal(GC, tGCvar, 1))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1125 return returnval
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1126
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1127
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1128 def reachableGC(C_struct):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1129 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1130 Checks if a demanded GC target content is reachable in dependence with the given sequence constraint.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1131 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1132 AU = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1133 for i in C_struct:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1134 if i == "A" or i == "U":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1135 AU += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1136 maxGC = 1 - (AU / float(len(C_struct))) # 1 - min_GC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1137 return maxGC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1138
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1139
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1140 def runColony(s, SC, objective_to_target_distance, GC, alpha, beta, evaporation_rate, correction_terms, verbose, IUPAC, IUPAC_compatibles, degreeOfSequenceInducement, IUPAC_reverseComplements, termination_convergence, convergence_count, reset_limit, improve, temperature, paramFile, pseudoknots, strategy):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1141 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1142 Execution function of a single ant colony finding one solution sequence
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1143 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1144 retString = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1145 retString2 = []
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1146 BPstack, LP = getBPStack(s, SC)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1147
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1148 rGC = reachableGC(SC)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1149 GC_message = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1150 if GC > rGC:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1151 print >> sys.stderr, "WARNING: Chosen target GC %s content is not reachable due to sequence constraint! Sequence Constraint GC-content is: %s" % (GC, rGC)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1152 GC = rGC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1153
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1154 # Initial Constraint Checks prior to execution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1155 STR = isValidStructure(s)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1156 START_SC , SC = checkSequenceConstraint(str(SC))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1157 START_LENGTH = checkSimilarLength(str(s), str(SC))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1158 START_constraint_compatibility , CompReport = checkConstaintCompatibility(BPstack, SC, IUPAC_compatibles)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1159
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1160 g2g = good2Go(START_SC, START_LENGTH, START_constraint_compatibility, STR)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1161 if (g2g == 1):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1162 start_time = time.time()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1163 max_time = 600 # seconds
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1164
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1165
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1166
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1167
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1168 ####
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1169 # INITIALIZATION OF THE RNA TOOLs
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1170 #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1171 RNAfold = init_RNAfold(213, temperature, paramFile)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1172 #RNAdistance = init_RNAdistance()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1173 RNAfold_pattern = re.compile('.+\n([.()]+)\s.+')
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1174 #RNAdist_pattern = re.compile('.*\s([\d]+)')
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1175 #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1176 ####
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1177
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1178 terrain = initTerrain(s)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1179 #print len(terrain),
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1180 terrain = applyTerrainModification(terrain, s, GC, SC, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1181 #print len(terrain[0])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1182 #printTerrain(terrain)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1183 #exit(0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1184 global_ant_count = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1185 global_best_ants = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1186 criterion = False
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1187 met = True
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1188 ant_no = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1189 prev_res = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1190 seq = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1191
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1192 counter = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1193
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1194 dstruct_log = []
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1195 dGC_log = []
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1196
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1197
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1198 distance_structural = 1000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1199 distance_GC = 1000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1200 distance_seq = 1000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1201
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1202 convergence = convergence_count
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1203 convergence_counter = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1204
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1205 resets = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1206
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1207 path = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1208 curr_structure = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1209
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1210 Dscore = 100000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1211 distance_structural = 10000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1212 distance_GC = 10000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1213 distance_seq = 10000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1214 best_solution = (path, curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1215 best_solution_local = (path, curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1216
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1217 best_solution_since = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1218
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1219 ants_per_selection = 10
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1220 if len(LP) > 0 :
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1221 for lp in LP:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1222 s = substr(lp + 1, s, ".")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1223 s = substr(LP[lp] + 1, s, ".")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1224
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1225 init = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1226 while criterion != met and getUsedTime(start_time) < max_time:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1227 iteration_start = time.time()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1228 global_ant_count += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1229 global_best_ants += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1230
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1231 path_info = getPathFromSelection(ants_per_selection, s, terrain, alpha, beta, RNAfold, RNAfold_pattern, GC, SC, LP, verbose, IUPAC_compatibles, degreeOfSequenceInducement, IUPAC_reverseComplements, IUPAC, pseudoknots, strategy)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1232
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1233 distance_structural_prev = distance_structural
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1234 distance_GC_prev = distance_GC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1235 distance_seq_prev = distance_seq
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1236
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1237 path, Dscore , distance_structural, distance_GC, distance_seq = path_info
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1238 curr_structure = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1239 if pseudoknots:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1240 curr_structure = getPKStructure(path, strategy)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1241 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1242 curr_structure = getRNAfoldStructure(path, RNAfold)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1243
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1244 curr_solution = (path,curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1245 # BEST SOLUTION PICKING
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1246 if improve == "h": # hierarchical check
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1247 # for the global best solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1248 if distance_structural < best_solution[3] or (distance_structural == best_solution[3] and distance_GC < best_solution[4]):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1249 best_solution = curr_solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1250 ant_no = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1251 # for the local (reset) best solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1252 if distance_structural < best_solution_local[3] or (distance_structural == best_solution_local[3] and distance_GC < best_solution_local[4]):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1253 best_solution_local = curr_solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1254
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1255 elif improve == "s": #score based check
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1256 # store best global solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1257 if Dscore < best_solution[2]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1258 best_solution = curr_solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1259 ant_no = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1260 # store best local solution for this reset
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1261 if Dscore < best_solution_local[2]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1262 best_solution_local = curr_solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1263
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1264 # OLD ' BEST SOLUTION ' PICKING
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1265 # if Dscore < best_solution[2]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1266 # best_solution = (path,curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1267 #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1268 # if Dscore < best_solution_local[2]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1269 # best_solution_local = (path,curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1270
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1271
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1272 distance_DN = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1273
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1274 if verbose:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1275 print "SCORE " + str(Dscore) + " Resets " + str(resets) + " #Ant " + str(global_ant_count) + " out of " + str(ants_per_selection) + " cc " + str(convergence_counter)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1276
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1277 print s, " <- target struct"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1278 print best_solution[0] , " <- BS since ", str(best_solution_since), "Size of Terrrain:", len(terrain[0])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1279 print best_solution[1] , " <- BS Dscore " + str(best_solution[2]) + " ds " + str(best_solution[3]) + " dGC " + str(best_solution[4]) + " dseq " + str(best_solution[5])+ " LP " + str(len(LP)) + " <- best solution stats"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1280 print curr_structure, " <- CS"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1281 print path,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1282 print " <- CS", "Dscore", str(Dscore), "ds", distance_structural, "dGC", distance_GC, "GC", getGC(path)*100, "Dseq", distance_seq
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1283
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1284 #### UPDATING THE TERRAIN ACCORDING TO THE QUALITY OF THE CURRENT BESTO-OUT-OF-k SOLUTION
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1285 updateTerrain(path, curr_structure, s, distance_structural,distance_GC, distance_seq, distance_DN, terrain, evaporation_rate, correction_terms, BPstack, verbose, global_ant_count)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1286 ####
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1287 if verbose: print "Used time for one iteration", time.time() - iteration_start
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1288
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1289
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1290 # CONVERGENCE AND TERMINATION CRITERION MANAGEMENT
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1291 #print distance_structural, distance_GC, best_solution_local[3], best_solution_local[4]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1292 if inConvergenceCorridor(curr_solution[3], curr_solution[4], best_solution_local[3], best_solution_local[4]):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1293 convergence_counter += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1294 if distance_structural_prev == distance_structural and distance_GC_prev == distance_GC:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1295 convergence_counter += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1296
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1297 if best_solution[3] == objective_to_target_distance:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1298 if best_solution[4] == 0.0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1299 break
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1300 ant_no = ant_no + 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1301 convergence_counter -= 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1302 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1303 ant_no = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1304
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1305
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1306 if ant_no == termination_convergence or resets >= reset_limit or global_ant_count >= 100000 or best_solution_since == 5:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1307 break
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1308
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1309 # RESET
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1310 if ant_no < termination_convergence and convergence_counter >= convergence:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1311
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1312 terrain = initTerrain(s)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1313 terrain = applyTerrainModification(terrain, s, GC, SC, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1314 criterion = False
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1315 met = True
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1316 ant_no = 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1317 prev_res = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1318 pre_path = "_" * len(s)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1319 path = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1320 curr_structure = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1321 counter = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1322 Dscore = 100000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1323 distance_structural = 1000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1324 distance_GC = 1000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1325 distance_seq = 1000
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1326 best_solution_local = (path, curr_structure, Dscore, distance_structural, distance_GC, distance_seq)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1327 convergence = convergence_count
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1328 convergence_counter = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1329
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1330 if resets == 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1331 sentinel_solution = best_solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1332 best_solution_since += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1333 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1334 if best_solution[2] < sentinel_solution[2]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1335 sentinel_solution = best_solution
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1336 best_solution_since = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1337 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1338 best_solution_since += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1339
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1340 resets += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1341
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1342 duration = getUsedTime(start_time)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1343
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1344 retString += "\|Ants:" + str(global_ant_count)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1345 retString += "\|Resets:" + str(resets) + "/" + str(reset_limit)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1346 retString += "\|AntsTC:" + str(termination_convergence)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1347 retString += "\|CC:" + str(convergence_count)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1348 retString += "\|IP:" + str(improve)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1349 retString += "\|BSS:" + str(best_solution_since)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1350 #if GC_message != "":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1351 # retString += GC_message + "\n"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1352
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1353 sequence = best_solution[0]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1354 struct = best_solution[1]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1355
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1356 retString += "\|LP:" + str(len(LP))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1357 retString += "\|ds:" + str(getStructuralDistance(s,SC, sequence, RNAfold, verbose, LP, BPstack, RNAfold_pattern, IUPAC_compatibles, degreeOfSequenceInducement, pseudoknots, strategy))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1358 retString += "\|dGC:" + str(best_solution[4])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1359 retString += "\|GC:" + str(getGC(sequence)*100)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1360 retString += "\|dseq:" + str(getSequenceEditDistance(SC, sequence))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1361 retString += "\|L:" + str(len(sequence))
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1362 retString += "\|Time:" + str(duration)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1363
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1364 retString2.append(struct)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1365 retString2.append(sequence)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1366
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1367 # CLOSING THE PIPES TO THE PROGRAMS
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1368 RNAfold.communicate()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1369 #RNAdistance.communicate()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1370
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1371 else: # Structural premisses are not met, htherefore the program will halt with a failure message
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1372 retString += "\nSome mistake detected\n"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1373 retString += "SequenceConstraintCheck: " + str(START_SC) + "\nSequenceConstraint: " + str(SC) + "\nLengthCheck: " + str(START_LENGTH) + "\nConstraintCompatibility: " + str(START_constraint_compatibility)+ "\n" + CompReport + "\n"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1374
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1375 return (retString, retString2)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1376
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1377 def findSequence(structure, Cseq, tGC, colonies, name, alpha, beta, evaporation_rate, struct_correction_term, GC_correction_term, seq_correction_term, degreeOfSequenceInducement, file_id, verbose, output_verbose, tGCmax, tGCvar, termination_convergence, convergence_count, reset_limit, improve, seed, temperature, paramFile, pseudoknots, strategy, useGU, return_mod = False):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1378 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1379 MAIN antaRNA - ant assembled RNA
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1380 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1381
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1382 if seed != "none":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1383 random.seed(seed)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1384
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1385 if Cseq == "":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1386 sequenceconstraint = "N" * len(structure)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1387 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1388 sequenceconstraint = str(Cseq)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1389
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1390 alpha = float(alpha)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1391 beta = float(beta)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1392 tGC = float(tGC)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1393 evaporation_rate = float(evaporation_rate)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1394 struct_correction_term = float(struct_correction_term)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1395 GC_correction_term = float(GC_correction_term)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1396 seq_correction_term = float(seq_correction_term)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1397 colonies = int(colonies)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1398 file_id = str(file_id)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1399 tmp_verbose = verbose
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1400 tmp_output_verbose = output_verbose
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1401 verbose = tmp_output_verbose # Due to later change, this is a twistaround and a switching of purpose
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1402 output_verbose = tmp_verbose # Due to later change, this is a twistaround and a switching of purpose
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1403 correction_terms = struct_correction_term, GC_correction_term, seq_correction_term
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1404 temperature = float(temperature)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1405 print_to_STDOUT = (file_id == "STDOUT")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1406
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1407 useGU = useGU
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1408
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1409 if return_mod == False:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1410 if print_to_STDOUT == False:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1411 outfolder = '/'.join(file_id.strip().split("/")[:-1])
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1412 curr_dir = os.getcwd()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1413 if not os.path.exists(outfolder):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1414 os.makedirs(outfolder)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1415 os.chdir(outfolder)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1416
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1417
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1418 sequenceconstraint = transform(sequenceconstraint)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1419 ###############################################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1420
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1421 # Allowed deviation from the structural target:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1422 objective_to_target_distance = 0.0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1423
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1424 # Loading the IUPAC copatibilities of nuleotides and their abstract representing symbols
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1425 IUPAC = {"A":"A", "C":"C", "G":"G", "U":"U", "R":"AG", "Y":"CU", "S":"GC", "W":"AU","K":"GU", "M":"AC", "B":"CGU", "D":"AGU", "H":"ACU", "V":"ACG", "N":"ACGU"}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1426 IUPAC_compatibles = loadIUPACcompatibilities(IUPAC, useGU)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1427
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1428 IUPAC_reverseComplements = {}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1429 if useGU == False: ## Without the GU basepair
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1430 IUPAC_reverseComplements = {"A":"U", "C":"G", "G":"C", "U":"A", "R":"UC", "Y":"AG", "S":"GC", "W":"UA","K":"CA", "M":"UG", "B":"AGC", "D":"ACU", "H":"UGA", "V":"UGC", "N":"ACGU"}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1431 else: ## allowing the GU basepair
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1432 IUPAC_reverseComplements = {"A":"U", "C":"G", "G":"UC", "U":"AG", "R":"UC", "Y":"AG", "S":"UGC", "W":"UAG","K":"UCAG", "M":"UG", "B":"AGCU", "D":"AGCU", "H":"UGA", "V":"UGC", "N":"ACGU"}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1433
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1434 result = []
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1435 for col in xrange(colonies):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1436 # Checking the kind of taget GC value should be used
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1437 GC = getGCSamplingValue(tGC, tGCmax, tGCvar)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1438
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1439 # Actual execution of a ant colony procesdure
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1440 output_v, output_w = runColony(structure, sequenceconstraint, objective_to_target_distance, GC, alpha, beta, evaporation_rate, correction_terms, verbose, IUPAC, IUPAC_compatibles, degreeOfSequenceInducement, IUPAC_reverseComplements, termination_convergence, convergence_count, reset_limit, improve, temperature, paramFile, pseudoknots, strategy)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1441
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1442 # Post-Processing the output of a ant colony procedure
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1443 line = ">" + name + str(col)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1444 if output_verbose:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1445 line += "\|Cstr:" + structure + "\|Cseq:" + sequenceconstraint + "\|Alpha:" + str(alpha) + "\|Beta:" + str(beta) + "\|tGC:" + str(GC) + "\|ER:" + str(evaporation_rate) + "\|Struct_CT:" + str(struct_correction_term) + "\|GC_CT:" + str(GC_correction_term) + "\|Seq_CT:" + str(seq_correction_term) + output_v + "\n" + "\n".join(output_w)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1446 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1447 line += "\n" + output_w[1]
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1448 if return_mod == False:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1449 if print_to_STDOUT:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1450 print line
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1451 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1452 if col == 0:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1453 print2file(file_id, line, 'w')
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1454 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1455 print2file(file_id, line, 'a')
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1456 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1457 result.append(line)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1458
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1459 if return_mod == True:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1460 return result
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1461 if print_to_STDOUT == False:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1462 os.chdir(curr_dir)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1463
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1464 def execute(args):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1465 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1466 CHECK AND PARSE THE COMMAND LINE STUFF
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1467 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1468
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1469 # Checking the arguments, parsed from the shell
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1470 ###############################################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1471 name = args.name
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1472 structure = args.Cstr
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1473
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1474 if args.Cseq == "":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1475 sequenceconstraint = "N" * len(structure)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1476 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1477 sequenceconstraint = args.Cseq
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1478
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1479 seed = args.seed
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1480
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1481
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1482 alpha = args.alpha
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1483 beta = args.beta
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1484 tGC = args.tGC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1485 if tGC < 0 or tGC > 1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1486 print "Error: Chosen tGC not in range [0,1]"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1487 exit(1)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1488 evaporation_rate = args.ER
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1489 struct_correction_term = args.Cstrweight
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1490 GC_correction_term = args.Cgcweight
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1491 seq_correction_term = args.Cseqweight
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1492 colonies = args.noOfColonies
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1493 degreeOfSequenceInducement = args.level
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1494 file_id = args.output_file
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1495 verbose = args.verbose
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1496 output_verbose = args.output_verbose
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1497
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1498 tGCmax = args.tGCmax
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1499 tGCvar = args.tGCvar
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1500
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1501 termination_convergence = args.antsTerConv
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1502 convergence_count = args.ConvergenceCount
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1503 temperature = args.temperature
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1504 reset_limit = args.Resets
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1505
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1506 improve = args.improve_procedure
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1507
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1508 ### RNAfold parameterfile
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1509 paramFile = args.paramFile
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1510
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1511 # Using the pkiss program under user changeable parameters
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1512 pseudoknots = args.pseudoknots
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1513
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1514 # Loading the optimized parameters for pseudoknots and ignore user input
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1515 if args.pseudoknot_parameters:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1516 alpha = 1.0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1517 beta = 0.1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1518 evaporation_rate = 0.2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1519 struct_correction_term = 0.1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1520 GC_correction_term = 1.0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1521 seq_correction_term = 0.5
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1522 termination_convergence = 50
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1523 convergence_count = 100
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1524
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1525
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1526 strategy = args.strategy
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1527 useGU = args.useGUBasePair
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1528
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1529 checkForViennaTools()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1530 if pseudoknots:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1531 checkForpKiss()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1532 findSequence(structure, sequenceconstraint, tGC, colonies, name, alpha, beta, evaporation_rate, struct_correction_term, GC_correction_term, seq_correction_term, degreeOfSequenceInducement, file_id, verbose, output_verbose, tGCmax, tGCvar, termination_convergence, convergence_count, reset_limit, improve, seed, temperature, paramFile, pseudoknots, strategy, useGU)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1533
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1534
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1535 def exe():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1536 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1537 MAIN EXECUTABLE WHICH PARSES THE INPUT LINE
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1538 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1539
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1540 argument_parser = argparse.ArgumentParser(
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1541 description = """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1542
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1543 #########################################################################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1544 # antaRNA - ant assembled RNA #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1545 # -> Ant Colony Optimized RNA Sequence Design #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1546 # ------------------------------------------------------------ #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1547 # Robert Kleinkauf (c) 2015 #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1548 # Bioinformatics, Albert-Ludwigs University Freiburg, Germany #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1549 #########################################################################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1550
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1551 - For antaRNA only the VIENNNA RNA Package must be installed on your linux system.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1552 antaRNA will only check, if the executables of RNAfold and RNAdistance of the ViennaRNA package can be found. If those programs are
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1553 not installed correctly, no output will be generated, an also no warning will be prompted.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1554 So the binary path of the Vienna Tools must be set up correctly in your system's PATH variable in order to run antaRNA correctly!
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1555
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1556 - antaRNA was only tested under Linux.
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1557
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1558 - For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1559
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1560 """,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1561
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1562 epilog = """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1563 Example calls:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1564 python antaRNA.py --Cstr "...(((...)))..." --tGC 0.5 -n 2
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1565 python antaRNA.py --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1566 python antaRNA.py --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1567
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1568 #########################################################################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1569 # --- Hail to the Queen!!! All power to the swarm!!! --- #
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1570 #########################################################################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1571 """,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1572 #formatter_class=RawTextHelpFormatter
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1573 )
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1574
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1575 # mandatorys
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1576 argument_parser.add_argument("-Cstr", "--Cstr", help="Structure constraint using RNA dotbracket notation with fuzzy block constraint. \n(TYPE: %(type)s)\n\n", type=str, required=True)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1577 argument_parser.add_argument("-tGC", "--tGC", help="Objective target GC content in [0,1].\n(TYPE: %(type)s)\n\n", type=float, required=True)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1578 argument_parser.add_argument("-n", "--noOfColonies", help="Number of sequences which shall be produced. \n(TYPE: %(type)s)\n\n\n\n", type=int, default=1)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1579 argument_parser.add_argument("-GU", "--useGUBasePair", help="Allowing GU base pairs. \n\n", action="store_true")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1580
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1581 argument_parser.add_argument("-s", "--seed", help = "Provides a seed value for the used pseudo random number generator.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="none")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1582 argument_parser.add_argument("-ip", "--improve_procedure", help = "Select the improving method. h=hierarchical, s=score_based.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="s")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1583 argument_parser.add_argument("-r", "--Resets", help = "Amount of maximal terrain resets, until the best solution is retuned as solution.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=int, default=5)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1584 argument_parser.add_argument("-CC", "--ConvergenceCount", help = "Delimits the convergence count criterion for a reset.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=int, default=130)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1585 argument_parser.add_argument("-aTC", "--antsTerConv", help = "Delimits the amount of internal ants for termination convergence criterion for a reset.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=int, default=50)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1586
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1587 argument_parser.add_argument("-p", "--pseudoknots", help = "Switch to pseudoknot based prediction using pKiss. Check the pseudoknot parameter usage!!!\n\n", action="store_true")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1588 argument_parser.add_argument("-pkPar", "--pseudoknot_parameters", help = "Enable optimized parameters for the usage of pseudo knots (Further parameter input ignored).\n\n", action="store_true")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1589 argument_parser.add_argument("--strategy", help = "Defining the pKiss folding strategy.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="A")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1590
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1591 # Mutual Exclusiv target GC distribution variables
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1592 #tGCgroup = argument_parser.add_mutually_exclusive_group()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1593 argument_parser.add_argument("-tGCmax", "--tGCmax", help = "Provides a maximum tGC value [0,1] for the case of uniform distribution sampling. The regular tGC value serves as minimum value.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=-1.0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1594 argument_parser.add_argument("-tGCvar", "--tGCvar", help = "Provides a tGC variance (sigma square) for the case of normal distribution sampling. The regular tGC value serves as expectation value (mu).\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=-1.0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1595
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1596 argument_parser.add_argument("-t", "--temperature", help = "Provides a temperature for the folding algorithms.\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=37.0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1597 argument_parser.add_argument("-P", "--paramFile", help = "Changes the energy parameterfile of RNAfold. If using this explicitly, please provide a suitable energy file delivered by RNAfold. \n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1598 argument_parser.add_argument("-of","--output_file", help="Provide a path and an output file, e.g. \"/path/to/the/target_file\". \n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="STDOUT")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1599 argument_parser.add_argument("-Cseq", "--Cseq", help="Sequence constraint using RNA nucleotide alphabet {A,C,G,U} and wild-card \"N\". \n(TYPE: %(type)s)\n\n", type=str, default = "")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1600 argument_parser.add_argument("-l", "--level", help="Sets the level of allowed influence of sequence constraint on the structure constraint [0:no influence; 3:extensive influence].\n(TYPE: %(type)s)\n\n", type=int, default = 1)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1601 argument_parser.add_argument("--name", help="Defines a name which is used in the sequence output. \n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=str, default="antaRNA_")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1602 argument_parser.add_argument("-a", "--alpha", help="Sets alpha, probability weight for terrain pheromone influence. [0,1] \n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=1.0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1603 argument_parser.add_argument("-b", "--beta", help="Sets beta, probability weight for terrain path influence. [0,1]\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=1.0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1604 argument_parser.add_argument("-er", "--ER", help="Pheromone evaporation rate. \n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=0.2)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1605 argument_parser.add_argument("-Cstrw", "--Cstrweight", help="Structure constraint quality weighting factor. [0,1]\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=0.5)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1606 argument_parser.add_argument("-Cgcw", "--Cgcweight", help="GC content constraint quality weighting factor. [0,1]\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n", type=float, default=5.0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1607 argument_parser.add_argument("-Cseqw", "--Cseqweight", help="Sequence constraint quality weighting factor. [0,1]\n(DEFAULT: %(default)s, TYPE: %(type)s)\n\n\n", type=float, default=1.0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1608 argument_parser.add_argument("-ov", "--output_verbose", help="Displayes intermediate output.\n\n", action="store_true")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1609 argument_parser.add_argument("-v", "--verbose", help="Prints additional features and stats to the headers of the produced sequences. Also adds the structure of the sequence.\n\n", action="store_true")
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1610
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1611 args = argument_parser.parse_args()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1612
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1613 execute(args)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1614
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1615 def checkForViennaTools():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1616 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1617 Checking for the presence of the Vienna tools in the system by which'ing for RNAfold and RNAdistance
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1618 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1619 RNAfold_output = subprocess.Popen(["which", "RNAfold"], stdout=subprocess.PIPE).communicate()[0].strip()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1620 if len(RNAfold_output) > 0 and RNAfold_output.find("found") == -1 and RNAfold_output.find(" no ") == -1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1621 return True
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1622 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1623 print "It seems the Vienna RNA Package is not installed on your machine. Please do so!"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1624 print "You can get it at http://www.tbi.univie.ac.at/"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1625 exit(0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1626
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1627
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1628 def checkForpKiss():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1629 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1630 Checking for the presence of pKiss
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1631 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1632 pKiss_output = subprocess.Popen(["which", "pKiss"], stdout=subprocess.PIPE).communicate()[0].strip()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1633 if len(pKiss_output) > 0 and pKiss_output.find("found") == -1 and pKiss_output.find(" no ") == -1:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1634 return True
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1635 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1636 print "It seems that pKiss is not installed on your machine. Please do so!"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1637 print "You can get it at http://bibiserv2.cebitec.uni-bielefeld.de/pkiss"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1638 exit(0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1639
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1640
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1641
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1642 if __name__ == "__main__":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1643
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1644 exe()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty rnateam parents: diff changeset	1645

Mercurial > repos > rnateam > antarna

annotate antaRNA.py @ 2:cfe9e6771518 draft default tip