Mercurial > repos > jay > pdaug_peptide_data_access
view PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py @ 0:6c12ca9f5d88 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 01:59:25 +0000 |
parents | |
children | f85327600c11 |
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import os import argparse def TSVtoFASTA(InFile, Method, Positive, Negative, OutFile): if Method == 'WithClassLabel': f = open(InFile) lines = f.readlines() of1 = open(Positive,'w') of2 = open(Negative,'w') n = 0 m = 0 for line in lines: if '1' in line.split('\t')[1].strip('\n'): n= n+1 of1.write('>peptide_'+str(n)+'\n') of1.write(line.split('\t')[0]+'\n') if '0' in line.split('\t')[1].strip('\n'): m= m+1 of2.write('>peptide_'+str(m)+'\n') of2.write(line.split('\t')[0]+'\n') elif Method == 'NoClassLabel': f = open(InFile) lines = f.readlines() of1 = open(OutFile,'w') for i, line in enumerate(lines[1:]): of1.write('>peptide_'+str(i)+'\n') of1.write(line.split('\t')[0]+'\n') else: pass if __name__=="__main__": import argparse 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("-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)