Mercurial > repos > jay > pdaug_peptide_sequence_analysis

comparison PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py @ 1:017c42b567ac draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
author jay
date Tue, 29 Dec 2020 03:51:51 +0000
parents e59674e3a391
children 79b1b090990b
comparison
equal deleted inserted replaced
0:e59674e3a391 1:017c42b567ac
12 of1 = open(Positive,'w') 12 of1 = open(Positive,'w')
13 of2 = open(Negative,'w') 13 of2 = open(Negative,'w')
14 14
15 n = 0 15 n = 0
16 m = 0 16 m = 0
17
18 l = []
19
20 for line in lines[1:]:
21 l.append(line.split('\t')[1].strip('\n').strip('\r'))
22 l = list(set(l))
17 23
18 for line in lines: 24 for line in lines:
19 25
20 if '1' in line.split('\t')[1].strip('\n'): 26 if l[0] in line.split('\t')[1].strip('\n').strip('\r'):
21 n= n+1 27 n= n+1
22 of1.write('>peptide_'+str(n)+'\n') 28 of1.write('>peptide_'+str(n)+'_'+str(l[0])+'\n')
23 of1.write(line.split('\t')[0]+'\n') 29 of1.write(line.split('\t')[0]+'\n')
24 30
25 if '0' in line.split('\t')[1].strip('\n'): 31 if l[1] in line.split('\t')[1].strip('\n').strip('\r'):
26 m= m+1 32 m= m+1
27 of2.write('>peptide_'+str(m)+'\n') 33 of2.write('>peptide_'+str(m)+'_'+str(l[1])+'\n')
28 of2.write(line.split('\t')[0]+'\n') 34 of2.write(line.split('\t')[0]+'\n')
29 35
30 elif Method == 'NoClassLabel': 36 elif Method == 'NoClassLabel':
31 37
32 f = open(InFile) 38 f = open(InFile)
45 import argparse 51 import argparse
46 52
47 parser = argparse.ArgumentParser() 53 parser = argparse.ArgumentParser()
48 54
49 parser.add_argument("-I", "--InFile", required=True, default=None, help=".fasta or .tsv") 55 parser.add_argument("-I", "--InFile", required=True, default=None, help=".fasta or .tsv")
50 parser.add_argument("-P", "--Postvs", required=False, default='Positive.fasta', help="Path to target tsv file") 56 parser.add_argument("-P", "--Postvs", required=False, default='FirstDataFile.fasta', help="Path to target tsv file")
51 parser.add_argument("-N", "--Negtvs", required=False, default='Negative.fasta', help="Path to target tsv file") 57 parser.add_argument("-N", "--Negtvs", required=False, default='SecondDataFile.fasta', help="Path to target tsv file")
52 parser.add_argument("-O", "--OutFile", required=False, default='OutFile.fasta', help="Path to target tsv file") 58 parser.add_argument("-O", "--OutFile", required=False, default='OutFile.fasta', help="Path to target tsv file")
53 parser.add_argument("-M", "--Method", required=True, default=None, help="Path to target tsv file") 59 parser.add_argument("-M", "--Method", required=True, default=None, help="Path to target tsv file")
54 args = parser.parse_args() 60 args = parser.parse_args()
55 61
56 TSVtoFASTA(args.InFile, args.Method, args.Postvs, args.Negtvs, args.OutFile) 62 TSVtoFASTA(args.InFile, args.Method, args.Postvs, args.Negtvs, args.OutFile)
57