Mercurial > repos > jay > pdaug_tsvtofasta

annotate PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.py @ 7:e9fa3b6346e3 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit f712b6b476db199167e49c52abab86e05f1fe815"
author jay
date Wed, 13 Jan 2021 20:46:05 +0000
parents e873a5224d1e
children
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1 import modlamp
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2 from modlamp.datasets import load_AMPvsTM
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3 from modlamp.datasets import load_AMPvsUniProt
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4 from modlamp.datasets import load_ACPvsTM
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5 from modlamp.datasets import load_ACPvsRandom
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6 from modlamp.database import query_apd
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7 from modlamp.database import query_camp
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8 import os
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9 import pandas as pd
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11 def DataGen(DataBaseType, OutFile, IDs):
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12
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13 if DataBaseType == 'AMPvsTMP':
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14 data = load_AMPvsTM()
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16 elif DataBaseType == 'AMPvsUniProt':
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17 data = load_AMPvsUniProt()
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19 elif DataBaseType == 'ACPvsTMP':
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20 data = load_ACPvsTM()
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22 elif DataBaseType == 'ACPvsRandom':
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23 data = load_ACPvsRandom()
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25 elif DataBaseType == 'query_apd':
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27 data = query_apd([int(i) for i in IDs.split(',')])
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28 df = pd.DataFrame(data, columns=['Peptides'])
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29 df.to_csv(OutFile, index=False, sep='\t')
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30 exit()
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32 elif DataBaseType == 'query_camp':
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33 data = query_camp([int(i) for i in IDs.split(',')])
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34 df = pd.DataFrame(data, columns=['Peptides'])
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35 df.to_csv(OutFile, index=False, sep='\t')
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36 exit()
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38 else:
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39 print ("Enter Correct Values")
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40 exit()
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41
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42 peptide_data = data.sequences
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43 class_label = int(len(peptide_data)/2)*[data.target_names[0]]+int(len(peptide_data)/2)*[data.target_names[1]]
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44 peptide_data = pd.DataFrame(peptide_data, columns=['name'])
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45 class_label = pd.DataFrame(class_label, columns=['class_label'])
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46 df = pd.concat([peptide_data,class_label], axis=1)
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48 df.to_csv(OutFile, index=False, sep='\t')
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50
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51 if __name__=="__main__":
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52
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53 import argparse
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54 parser = argparse.ArgumentParser()
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55
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56 parser.add_argument("-d", "--DataBaseType",
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57 required=True,
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58 default=None,
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59 help="Name of the dataset ")
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60
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61 parser.add_argument("-o", "--OutFile",
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62 required=False,
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63 default='Out.tsv',
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64 help="Out put file name for str descriptors")
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66 parser.add_argument("-L", "--List",
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67 required=False,
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68 default=None,
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69 help="List of integer as ID")
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71 args = parser.parse_args()
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72 DataGen(args.DataBaseType, args.OutFile, args.List)