Mercurial > repos > cpt > cpt_putative_isp

comparison generate-putative-isp.py @ 3:08499fbf8697 draft

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planemo upload commit 96d9c038cdd9f83fcc55d2f20ab1057129d11589-dirty
author cpt
date Wed, 18 Sep 2024 04:02:06 +0000
parents 4e02e6e9e77d
children bc16792ecfd2
comparison
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2:0a02ef22ce17 3:08499fbf8697
3 ##### findSpanin.pl --> findSpanin.py 3 ##### findSpanin.pl --> findSpanin.py
4 ######### Incooperated from the findSpanin.pl script, but better and more snakey. 4 ######### Incooperated from the findSpanin.pl script, but better and more snakey.
5 5
6 import argparse 6 import argparse
7 from cpt import OrfFinder 7 from cpt import OrfFinder
8 from Bio import SeqIO
9 from Bio import Seq
10 import re 8 import re
11 from spaninFuncs import * 9 from spaninFuncs import *
12 import os 10
13
14 # if __name__ == '__main__':
15 # pass
16 ###############################################################################
17 11
18 if __name__ == "__main__": 12 if __name__ == "__main__":
19
20 # Common parameters for both ISP / OSP portion of script
21 13
22 parser = argparse.ArgumentParser( 14 parser = argparse.ArgumentParser(
23 description="Get putative protein candidates for spanins" 15 description="Get putative protein candidates for spanins"
24 ) 16 )
25 parser.add_argument( 17 parser.add_argument(
210 args.out_isp_prot.close() 202 args.out_isp_prot.close()
211 args.out_isp_prot = open(args.out_isp_prot.name, "r") 203 args.out_isp_prot = open(args.out_isp_prot.name, "r")
212 204
213 pairs = tuple_fasta(fasta_file=args.out_isp_prot) 205 pairs = tuple_fasta(fasta_file=args.out_isp_prot)
214 206
215 # print(pairs)
216
217 have_tmd = [] # empty candidates list to be passed through the user input criteria 207 have_tmd = [] # empty candidates list to be passed through the user input criteria
218 208
219 for ( 209 for each_pair in pairs:
220 each_pair
221 ) in (
222 pairs
223 ): # grab transmembrane domains from spaninFuncts (queries for lysin snorkels # and a range of hydrophobic regions that could be TMDs)
224 if len(each_pair[1]) <= args.max_isp: 210 if len(each_pair[1]) <= args.max_isp:
225 try: 211 try:
226 have_tmd += find_tmd( 212 have_tmd += find_tmd(
227 pair=each_pair, 213 pair=each_pair,
228 minimum=args.isp_min_dist, 214 minimum=args.isp_min_dist,