Mercurial > repos > jay > pdaug_peptide_cd_spectral_analysis

annotate PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py @ 4:348ac90203a3 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
author jay
date Tue, 12 Jan 2021 19:54:04 +0000
parents 974ba4a94895
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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2 import pandas as pd
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5 def TSVtoFASTA(infile, method, firstdatafile, seconddatafile, outfile, clmpepid, slcclasslabel, peps):
348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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8 fn = [firstdatafile, seconddatafile]
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11 df = pd.read_csv(infile, sep="\t")
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12 if clmpepid == None:
348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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13 pass
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14 else:
348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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15 names = df[clmpepid].tolist()
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17 peps = df[peps].tolist()
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19 if method == "withoutlabel":
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20 f = open(outfile,'w')
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21 if clmpepid is not None:
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22 for i,n in enumerate(peps):
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23 f.write(">"+names[i]+'\n')
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24 f.write(n+'\n')
348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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25 f.close()
348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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26 else:
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27 for i,n in enumerate(peps):
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28 f.write(">"+str(i)+'\n')
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29 f.write(n+'\n')
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30 f.close()
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32 elif method == "withlabel":
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33 labels = df[slcclasslabel].tolist()
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35 label = list(set(labels))
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37 if clmpepid is None:
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38 for i, l in enumerate(label):
348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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39 f = open(fn[i],'w')
348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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40 print('ok1')
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41 for i, L in enumerate(labels):
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42 if l == L:
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43 f.write(">"+str(i)+"_"+str(l)+'\n')
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44 f.write(peps[i]+'\n')
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45 f.close()
348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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46 else:
348ac90203a3 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
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47 for i, l in enumerate(label):
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48 f = open(fn[i],'w')
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49 for i, L in enumerate(labels):
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50 if l == L:
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51 f.write(">"+names[i]+"_"+l+'\n')
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52 f.write(peps[i]+'\n')
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53 f.close()
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55 if __name__=="__main__":
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57 import argparse
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58 parser = argparse.ArgumentParser()
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59 parser.add_argument("-I", "--InFile", required=True, default=None, help=".fasta or .tsv")
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60 parser.add_argument("-F", "--FirstDataFile", required=False, default='FirstDataFile.fasta', help="Path to target tsv file")
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61 parser.add_argument("-S", "--SecondDataFile", required=False, default='SecondDataFile.fasta', help="Path to target tsv file")
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62 parser.add_argument("-O", "--OutFile", required=False, default='OutFile.fasta', help="Path to target tsv file")
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63 parser.add_argument("-M", "--Method", required=True, default=None, help="Path to target tsv file")
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64 parser.add_argument("-C", "--ClmPepID", required=False, default=None, help="Peptide Column Name")
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65 parser.add_argument("-L", "--SlcClassLabel", required=False, default="Class_label", help="Class Label Column Name")
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66 parser.add_argument("-P", "--PeptideColumn", required=True, default=None, help="Class Label Column Name")
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67 args = parser.parse_args()
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69 TSVtoFASTA(args.InFile, args.Method, args.FirstDataFile, args.SecondDataFile, args.OutFile, args.ClmPepID, args.SlcClassLabel, args.PeptideColumn)
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