Mercurial > repos > jay > pdaug_peptide_ngrams

annotate PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py @ 0:7557b48b2872 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 02:10:12 +0000
parents
children 9b5e990a0ebb
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7557b48b2872 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 import os
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2 import argparse
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5 def TSVtoFASTA(InFile, Method, Positive, Negative, OutFile):
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7 if Method == 'WithClassLabel':
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9 f = open(InFile)
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10 lines = f.readlines()
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12 of1 = open(Positive,'w')
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13 of2 = open(Negative,'w')
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15 n = 0
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16 m = 0
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18 for line in lines:
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20 if '1' in line.split('\t')[1].strip('\n'):
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21 n= n+1
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22 of1.write('>peptide_'+str(n)+'\n')
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23 of1.write(line.split('\t')[0]+'\n')
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25 if '0' in line.split('\t')[1].strip('\n'):
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26 m= m+1
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27 of2.write('>peptide_'+str(m)+'\n')
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28 of2.write(line.split('\t')[0]+'\n')
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30 elif Method == 'NoClassLabel':
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32 f = open(InFile)
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33 lines = f.readlines()
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34 of1 = open(OutFile,'w')
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36 for i, line in enumerate(lines[1:]):
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37 of1.write('>peptide_'+str(i)+'\n')
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38 of1.write(line.split('\t')[0]+'\n')
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40 else:
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41 pass
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43 if __name__=="__main__":
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45 import argparse
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47 parser = argparse.ArgumentParser()
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49 parser.add_argument("-I", "--InFile", required=True, default=None, help=".fasta or .tsv")
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50 parser.add_argument("-P", "--Postvs", required=False, default='Positive.fasta', help="Path to target tsv file")
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51 parser.add_argument("-N", "--Negtvs", required=False, default='Negative.fasta', help="Path to target tsv file")
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52 parser.add_argument("-O", "--OutFile", required=False, default='OutFile.fasta', help="Path to target tsv file")
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53 parser.add_argument("-M", "--Method", required=True, default=None, help="Path to target tsv file")
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54 args = parser.parse_args()
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56 TSVtoFASTA(args.InFile, args.Method, args.Postvs, args.Negtvs, args.OutFile)
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