Mercurial > repos > cpt > cpt_find_spanins

comparison spaninFuncs.py @ 5:46b252c89e9e draft

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planemo upload commit 25fff8b3887beeb66c2d53e2a32f9af9f34e40b6
author cpt
date Fri, 20 Sep 2024 04:19:02 +0000
parents fd70980a516b
children
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4:673d1776d3b9 5:46b252c89e9e
5 ###### Documentation will ATTEMPT to be thourough here 5 ###### Documentation will ATTEMPT to be thourough here
6 """ 6 """
7 7
8 import re 8 import re
9 from Bio import SeqIO 9 from Bio import SeqIO
10 from Bio import Seq
11 from collections import OrderedDict
12 10
13 # Not written in OOP for a LITTLE bit of trying to keep the complication down in case adjustments are needed by someone else. 11 # Not written in OOP for a LITTLE bit of trying to keep the complication down in case adjustments are needed by someone else.
14 # Much of the manipulation is string based; so it should be straightforward as well as moderately quick 12 # Much of the manipulation is string based; so it should be straightforward as well as moderately quick
15 ################## GLobal Variables 13 ################## GLobal Variables
16 Lys = "K" 14 Lys = "K"
517 for each_pair in pairs: 515 for each_pair in pairs:
518 # print(each_pair) 516 # print(each_pair)
519 # try: 517 # try:
520 try: 518 try:
521 lipo += find_lipobox(pair=each_pair, regex=2) # , minimum=8) 519 lipo += find_lipobox(pair=each_pair, regex=2) # , minimum=8)
522 except TypeError: # catches if something doesnt have the min/max requirements (something is too small) 520 except (
521 TypeError
522 ): # catches if something doesnt have the min/max requirements (something is too small)
523 continue 523 continue
524 # except: 524 # except:
525 # continue 525 # continue
526 # print('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n') 526 # print('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
527 #############################3 527 #############################3