Mercurial > repos > rnateam > antarna

annotate antaRNA.py @ 0:fcf4719d3831 draft

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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 11:02:53 -0400
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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
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2 import sys
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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3 import random
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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4 import subprocess
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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5 import re
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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6 import decimal
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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7 import math
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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8 import os
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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9 import shutil
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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10 import time
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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11 import types
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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12 import argparse
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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13 #from argparse import RawTextHelpFormatter
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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14
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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15 #############################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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16 # FUNCTIONS
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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17
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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19 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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21 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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22 line = str(i)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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23 if m == "a":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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24 call = "echo \"" + line + "\" >> " + f
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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25 elif m == "w":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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26 call = "echo \"" + line + "\" > " + f
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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27 os.system(call)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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28
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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30 def checkSequenceConstraint(SC):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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31 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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33 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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34 out = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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35 for c in SC:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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36 c = c.upper()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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39 if c == "T":
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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40 c = "U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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41 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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44 print "\tA Adenine"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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45 print "\tC Cytosine"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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46 print "\tG Guanine"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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58 print "\tN any base"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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59 exit(0)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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60 out += c
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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61 return (1, out)
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62
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63
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64 def transform(seq):
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65 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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67 """
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68 S = ""
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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69 for s in seq:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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70 if s == "T":
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71 S += "U"
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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72 else:
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73 S += s
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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74 return S
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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75
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76
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77 def checkSimilarLength(s, SC):
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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78 """
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79 Compares sequence and structure constraint length
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80 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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82 return 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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83 else:
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84 return 0
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85
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86
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87 def isStructure(s):
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88 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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89 Checks if the structure constraint only contains "(", ")", and "." and legal fuzzy structure constraint characters.
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90 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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91 returnvalue = 1
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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
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93 if s[a] not in ".()[]{}<>":
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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
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95 returnvalue = 0
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96 return returnvalue
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97
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98
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99 def isBalanced(s):
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100 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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101 Check if the structure s is of a balanced nature
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102 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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103
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104 balance = 1
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105 for bracket in ["()", "[]", "{}", "<>"]:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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106 counter = 0
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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108 if s[a] in bracket[0]:
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109 counter += 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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110 elif s[a] in bracket[1]:
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111 counter -= 1
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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112 if counter != 0:
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113 balance = 0
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114 return balance
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115
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116
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117
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118 def fulfillsHairpinRule(s):
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119 """
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120 CHECKING FOR THE 3 nt LOOP INTERSPACE
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121 for all kind of basepairs, even wihtin the pdeudoknots
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122 """
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123
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124 fulfillsRules = 1
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125 for bracket in ["()", "[]", "{}", "<>"]:
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126 last_opening_char = 0
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127 check = 0
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128 for a in xrange(len(s)):
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129 if s[a] == bracket[0]:
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130 last_opening_char = a
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131 check = 1
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132 elif s[a] == bracket[1] and check == 1:
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133 check = 0
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134 if a - last_opening_char < 4:
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135 return 0
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136 return 1
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137
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138
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139 def isValidStructure(s):
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140 """
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141 Checks, if the structure s is a valid structure
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142 """
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143
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144 Structure = isStructure(s)
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145 Balanced = isBalanced(s)
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146 HairpinRule = fulfillsHairpinRule(s)
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147
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148 if Structure == 1 and Balanced == 1 and HairpinRule == 1:
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149 return 1
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150 else:
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151 print Structure, Balanced, HairpinRule
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152 return 0
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153
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154 def loadIUPACcompatibilities(IUPAC, useGU):
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155 """
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156 Generating a hash containing all compatibilities of all IUPAC RNA NUCLEOTIDES
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157 """
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158 compatible = {}
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159 for nuc1 in IUPAC: # ITERATING OVER THE DIFFERENT GROUPS OF IUPAC CODE
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160 sn1 = list(IUPAC[nuc1])
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161 for nuc2 in IUPAC: # ITERATING OVER THE DIFFERENT GROUPS OF IUPAC CODE
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162 sn2 = list(IUPAC[nuc2])
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163 compatib = 0
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164 for c1 in sn1: # ITERATING OVER THE SINGLE NUCLEOTIDES WITHIN THE RESPECTIVE IUPAC CODE:
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165 for c2 in sn2: # ITERATING OVER THE SINGLE NUCLEOTIDES WITHIN THE RESPECTIVE IUPAC CODE:
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166 # CHECKING THEIR COMPATIBILITY
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167 if useGU == True:
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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
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169 compatib = 1
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170 else:
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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
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172 compatib = 1
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173 compatible[nuc1 + "_" + nuc2] = compatib # SAVING THE RESPECTIVE GROUP COMPATIBILITY, REVERSE SAVING IS NOT REQUIRED, SINCE ITERATING OVER ALL AGAINST ALL
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174 return compatible
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175
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176 def isCompatibleToSet(c1, c2, IUPAC_compatibles):
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177 """
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178 Checks compatibility of c1 wihtin c2
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179 """
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180 compatible = True
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181 for setmember in c2:
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182 #print setmember
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183 if isCompatible(c1, setmember, IUPAC_compatibles) == False:
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184 return False
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185 return compatible
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186
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187
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188 def isCompatible(c1, c2, IUPAC_compatibles):
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189 """
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190 Checks compatibility between character c1 and c2
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191 """
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192 if IUPAC_compatibles[c1 + "_" + c2] == 1:
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193 return True
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194 else:
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195 return False
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196
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197
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198 def isStructureCompatible(lp1, lp2 ,bp):
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199 """
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200 Checks, if the region within lp1 and lp2 is structurally balanced
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201 """
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202 x = lp1 + 1
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203 while (x < lp2):
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204 if (bp[x] <= lp1 or bp[x] > lp2):
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205 return False
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206 if x == bp[x]:
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207 x += 1
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208 else:
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209 x = bp[x] + 1
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210 return x == lp2
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211
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212
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213 def checkConstaintCompatibility(basepairstack, sequenceconstraint, IUPAC_compatibles):
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214 """
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215 Checks if the constraints are compatible to each other
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216 """
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217 returnstring = ""
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218 compatible = 1
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219 for id1 in basepairstack: # key = (constraint , (pos, constraint)))
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220 constr1 = basepairstack[id1][0]
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221 id2 = basepairstack[id1][1][0]
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222 constr2 = basepairstack[id1][1][1]
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223
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224 if id1 != id2 and not isCompatible(constr1, constr2, IUPAC_compatibles):
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225
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226 compatible = 0
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227 returnstring += "nucleotide constraint " + str(constr1) + " at position " + str(id1) + " is not compatible with nucleotide constraint " + str(constr2) + " at position " + str(id2) + "\n"
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228 #if not isCompatible(basepairstack[basepair][0], basepairstack[basepair][1][1]):
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229
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230 #compatible = 0
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231 #else:
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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"
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233 return (compatible, returnstring)
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234
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235
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236 def getLP(BPSTACK):
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237 """
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238 Retreives valid lonley base pairs from a base pair stack
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239 """
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240 #20 ('N', (>BLOCK<, 'N'))
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241
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242 # geting single base pairs
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243 stack = {}
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244 LP = {}
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245 if type(BPSTACK[random.choice(BPSTACK.keys())]) == types.TupleType:
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246 for i in BPSTACK.keys():
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247 #if str(BPSTACK[i][1][0]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
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248 stack[i] = int(BPSTACK[i][1][0])
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249 #print i , BPSTACK[i][1][0]
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250 else:
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251 for i in BPSTACK.keys():
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252 #if str(BPSTACK[i]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
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253 stack[i] = BPSTACK[i]
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254
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255 # removing redundant base pair indices
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256 for i in stack.keys():
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257 if i >= stack[i]:
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258 del stack[i]
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259
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260 # actual checking for single lonley base pairs
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261 for i in stack.keys():
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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):
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263 LP[i] = stack[i]
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264
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265 ##actual removal of 2er lonley base pairs
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266 for i in stack.keys():
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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):
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268 LP[i] = stack[i]
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269 LP[i+1] = stack[i+1]
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270
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271
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272 #if type(BPSTACK[random.choice(BPSTACK.keys())]) == types.TupleType:
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273 #for i in BPSTACK.keys():
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274
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275 ##if str(BPSTACK[i][1][0]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
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276 #stack[i] = int(BPSTACK[i][1][0])
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277 ##print i , BPSTACK[i][1][0]
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278 #else:
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279 #for i in BPSTACK.keys():
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280 ##if str(BPSTACK[i]) not in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
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281 #stack[i] = BPSTACK[i]
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282
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283 #for i in stack.keys():
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284 #if i >= stack[i]:
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285 #del stack[i]
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286
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287
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288
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289 return LP
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290
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291
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292 def getBPStack(s, seq):
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293 """
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294 Returns a dictionary of the corresponding basepairs of the structure s and the sequence constraint seq.
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295 """
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296 tmp_stack = {"()":[], "{}":[], "[]":[], "<>":[]}
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297 bpstack = {}
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298 for i in xrange(len(s)):
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299
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300 # REGULAR SECONDARY STRUCTURE DETECTION
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301 if s[i] in "(){}[]<>":
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302
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303 no = 0
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304 ### opening
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305 if s[i] in "([{<":
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306 if s[i] == "(":
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307 tmp_stack["()"].append((i, seq[i]))
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308 elif s[i] == "[":
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309 tmp_stack["[]"].append((i, seq[i]))
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310 elif s[i] == "{":
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311 tmp_stack["{}"].append((i, seq[i]))
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312 elif s[i] == "<":
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313 tmp_stack["<>"].append((i, seq[i]))
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314
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315 #closing
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316 elif s[i] in ")]}>":
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317 if s[i] == ")":
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318 no, constr = tmp_stack["()"].pop()
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319 elif s[i] == "]":
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320 no, constr = tmp_stack["[]"].pop()
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321 elif s[i] == "}":
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322 no, constr = tmp_stack["{}"].pop()
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323 elif s[i] == ">":
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324 no, constr = tmp_stack["<>"].pop()
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325 bpstack[no] = (constr, (i, seq[i]))
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326 bpstack[i] = (seq[i] ,(no, constr))
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327
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328 elif s[i] == ".":
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329 bpstack[i] = (seq[i], (i, seq[i]))
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330 elif s[i] in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
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331 bpstack[i] = (seq[i], (i, seq[i]))
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332
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333 return (bpstack, getLP(bpstack))
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334
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335
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336 def getbpStack(s):
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337 """
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338 Returns a dictionary of the corresponding basepairs of the structure s and the sequence constraint seq.
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339 """
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340 tmp_stack = {"()":[], "{}":[], "[]":[], "<>":[]}
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341 bpstack = {}
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342
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343 for i in xrange(len(s)):
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344 if s[i] in "(){}[]<>":
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345
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346 no = 0
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347 ### opening
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348 if s[i] in "([{<":
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349 if s[i] == "(":
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350 tmp_stack["()"].append(i)
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351 elif s[i] == "[":
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352 tmp_stack["[]"].append(i)
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353 elif s[i] == "{":
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354 tmp_stack["{}"].append(i)
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355 elif s[i] == "<":
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356 tmp_stack["<>"].append(i)
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357
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358 #closing
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359 elif s[i] in ")]}>":
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360 if s[i] == ")":
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361 no = tmp_stack["()"].pop()
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362 elif s[i] == "]":
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363 no = tmp_stack["[]"].pop()
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364 elif s[i] == "}":
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365 no = tmp_stack["{}"].pop()
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366 elif s[i] == ">":
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367 no = tmp_stack["<>"].pop()
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368 bpstack[no] = i # save basepair in the format {opening base id (opening seq constr,(closing base id, closing seq constr))}
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369 bpstack[i] = no # save basepair in the format {closing base id (closing seq constr,(opening base id, opening seq constr))}
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370
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371 elif s[i] == ".": # no structural constaint given: produce entry, which references itself as a base pair partner....
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372 bpstack[i] = i
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373
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374 elif s[i] in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
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375 bpstack[i] = i
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376
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377 #elif s[i] in "ABCDEFGHIJKLMNOPQRSTUVWXYZ":
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378 ## per position, assigned to a certain block, the target nucleotide, with whcih it should interact is marked with the specific
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379 ## block character
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380 #bpstack[i] = s[i]
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381
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382 return (bpstack, getLP(bpstack))
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383
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384 def maprange( a, b, s):
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385 """
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386 Mapping function
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387 """
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388 (a1, a2), (b1, b2) = a, b
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389 return b1 + ((s - a1) * (b2 - b1) / (a2 - a1))
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390
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391
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392 def applyGCcontributionPathAdjustment(pathlength, tmpGC, nt):
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393 """
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394 GC path length contribution calculation.
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395 """
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396 GCadjustment = 1.5
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397 minimum = 0.5
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398 upper = GCadjustment
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399 lower = minimum
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400
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401 if nt == "A" or nt == "U":
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402 pathlength = pathlength * maprange( (0, 1) , (lower, upper), tmpGC)
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403
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404 if nt == "G" or nt == "C":
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405 #pathlength = pathlength * (float(1-tmpGC))
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406 pathlength = pathlength * maprange( (1, 0) , (lower, upper), tmpGC)
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407 return pathlength
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408
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409 def getConstraint(TE, BPstack, IUPAC, IUPAC_compatibles, IUPAC_reverseComplements):
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410 """
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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)
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412 """
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413 # TE :: transition element / path section under dispute
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414 # id1 :: id of the position of the caharacter to which the transition is leading to
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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
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416 # val :: BPstack information of the specific position
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417 # constr1 :: constraining character of pos id1
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418 # constr2 :: constraining character of pos id2
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419
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420 id1 = int(TE.split(".")[0])
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421 val = BPstack[id1] # check out the value of the destination character in the basepair/constraint stack
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422 constr1 = val[0] # getting the constraint character of position id1
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423 id2 = int(val[1][0]) # getting position id2
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424 constr2 = val[1][1] # getting the sequence constraint for position id2
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425 targetNucleotide = TE.split(".")[1][-1:] # where the edge is leading to
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426
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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
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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
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diff changeset
1117 tGCmax = GC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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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
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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
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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
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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
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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
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diff changeset
1126
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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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
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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
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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
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diff changeset
1137 return maxGC
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1138
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1139
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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diff changeset
1141 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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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
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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
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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
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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
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diff changeset
1164
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1165
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diff changeset
1166
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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parents:
diff changeset
1177
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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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
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diff changeset
1363
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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diff changeset
1366
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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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
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diff changeset
1370
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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diff changeset
1376
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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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
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diff changeset
1380 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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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
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diff changeset
1387 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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diff changeset
1389
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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diff changeset
1406
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1407 useGU = useGU
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1408
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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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
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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
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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
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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
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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
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diff changeset
1416
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1417
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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diff changeset
1419 ###############################################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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1420
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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1423
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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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
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1427
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1428 IUPAC_reverseComplements = {}
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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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
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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
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1433
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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1434 result = []
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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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
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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
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1524
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diff changeset
1525
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1526 strategy = args.strategy
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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
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diff changeset
1528
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1529 checkForViennaTools()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1530 if pseudoknots:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1531 checkForpKiss()
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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diff changeset
1533
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1534
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1535 def exe():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1536 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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diff changeset
1538 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1539
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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
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diff changeset
1541 description = """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1542
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1543 #########################################################################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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diff changeset
1545 # -> Ant Colony Optimized RNA Sequence Design #
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diff changeset
1546 # ------------------------------------------------------------ #
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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
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diff changeset
1548 # Bioinformatics, Albert-Ludwigs University Freiburg, Germany #
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diff changeset
1549 #########################################################################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1550
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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
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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
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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
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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!
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1555
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1556 - antaRNA was only tested under Linux.
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1557
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diff changeset
1558 - For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/
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1559
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diff changeset
1560 """,
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1561
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1562 epilog = """
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1563 Example calls:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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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
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1567
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diff changeset
1568 #########################################################################
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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1570 #########################################################################
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1571 """,
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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1573 )
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1574
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diff changeset
1575 # mandatorys
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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
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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
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1579 argument_parser.add_argument("-GU", "--useGUBasePair", help="Allowing GU base pairs. \n\n", action="store_true")
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1580
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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")
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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")
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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)
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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)
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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)
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1586
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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")
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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
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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")
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1590
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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
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1592 #tGCgroup = argument_parser.add_mutually_exclusive_group()
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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
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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
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1595
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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)
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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="")
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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diff changeset
1610
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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diff changeset
1612
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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diff changeset
1613 execute(args)
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1614
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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diff changeset
1616 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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diff changeset
1618 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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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
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diff changeset
1622 else:
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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diff changeset
1626
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1627
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1628 def checkForpKiss():
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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diff changeset
1629 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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diff changeset
1631 """
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
rnateam
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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
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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
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parents:
diff changeset
1640
fcf4719d3831 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty
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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
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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