Mercurial > repos > jay > pdaug_sequence_based_peptide_generation

annotate PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py @ 2:cda6264267f7 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 8b18552f6d2b2261efebe1075ff4c18a295b94dd"
author jay
date Tue, 29 Dec 2020 19:00:54 +0000
parents d4075a2fc42b
children eab83d8fb156
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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 l = []
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20 for line in lines[1:]:
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21 l.append(line.split('\t')[1].strip('\n').strip('\r'))
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22 l = list(set(l))
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24 print(l)
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26 for line in lines:
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28 if l[1] in line.split('\t')[1].strip('\n').strip('\r'):
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29 n= n+1
1
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30 of1.write('>peptide_'+str(n)+'_'+str(l[0])+'\n')
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31 of1.write(line.split('\t')[0]+'\n')
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33 if l[0] in line.split('\t')[1].strip('\n').strip('\r'):
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34 m= m+1
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35 of2.write('>peptide_'+str(m)+'_'+str(l[1])+'\n')
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36 of2.write(line.split('\t')[0]+'\n')
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38 elif Method == 'NoClassLabel':
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40 f = open(InFile)
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41 lines = f.readlines()
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42 of1 = open(OutFile,'w')
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44 for i, line in enumerate(lines[1:]):
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45 of1.write('>peptide_'+str(i)+'\n')
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46 of1.write(line.split('\t')[0]+'\n')
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48 else:
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49 pass
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51 if __name__=="__main__":
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53 import argparse
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55 parser = argparse.ArgumentParser()
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57 parser.add_argument("-I", "--InFile", required=True, default=None, help=".fasta or .tsv")
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58 parser.add_argument("-P", "--Postvs", required=False, default='FirstDataFile.fasta', help="Path to target tsv file")
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59 parser.add_argument("-N", "--Negtvs", required=False, default='SecondDataFile.fasta', help="Path to target tsv file")
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60 parser.add_argument("-O", "--OutFile", required=False, default='OutFile.fasta', help="Path to target tsv file")
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61 parser.add_argument("-M", "--Method", required=True, default=None, help="Path to target tsv file")
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62 args = parser.parse_args()
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63
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64 TSVtoFASTA(args.InFile, args.Method, args.Postvs, args.Negtvs, args.OutFile)