Mercurial > repos > jay > pdaug_peptide_cd_spectral_analysis
diff PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py @ 1:9bbad349f44c draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
| author | jay |
|---|---|
| date | Tue, 29 Dec 2020 04:45:46 +0000 |
| parents | 6cff147419ab |
| children | 1c3b75d87fba |
line wrap: on
line diff
--- a/PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py Wed Oct 28 02:34:15 2020 +0000 +++ b/PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py Tue Dec 29 04:45:46 2020 +0000 @@ -14,17 +14,23 @@ n = 0 m = 0 + + l = [] + + for line in lines[1:]: + l.append(line.split('\t')[1].strip('\n').strip('\r')) + l = list(set(l)) for line in lines: - if '1' in line.split('\t')[1].strip('\n'): + if l[0] in line.split('\t')[1].strip('\n').strip('\r'): n= n+1 - of1.write('>peptide_'+str(n)+'\n') + of1.write('>peptide_'+str(n)+'_'+str(l[0])+'\n') of1.write(line.split('\t')[0]+'\n') - if '0' in line.split('\t')[1].strip('\n'): + if l[1] in line.split('\t')[1].strip('\n').strip('\r'): m= m+1 - of2.write('>peptide_'+str(m)+'\n') + of2.write('>peptide_'+str(m)+'_'+str(l[1])+'\n') of2.write(line.split('\t')[0]+'\n') elif Method == 'NoClassLabel': @@ -47,11 +53,10 @@ parser = argparse.ArgumentParser() parser.add_argument("-I", "--InFile", required=True, default=None, help=".fasta or .tsv") - parser.add_argument("-P", "--Postvs", required=False, default='Positive.fasta', help="Path to target tsv file") - parser.add_argument("-N", "--Negtvs", required=False, default='Negative.fasta', help="Path to target tsv file") + parser.add_argument("-P", "--Postvs", required=False, default='FirstDataFile.fasta', help="Path to target tsv file") + parser.add_argument("-N", "--Negtvs", required=False, default='SecondDataFile.fasta', help="Path to target tsv file") parser.add_argument("-O", "--OutFile", required=False, default='OutFile.fasta', help="Path to target tsv file") parser.add_argument("-M", "--Method", required=True, default=None, help="Path to target tsv file") args = parser.parse_args() - TSVtoFASTA(args.InFile, args.Method, args.Postvs, args.Negtvs, args.OutFile) - + TSVtoFASTA(args.InFile, args.Method, args.Postvs, args.Negtvs, args.OutFile) \ No newline at end of file