Mercurial > repos > jay > pdaug_sequence_similarity_network

annotate PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.py @ 0:e650de82bcc7 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 01:50:00 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e650de82bcc7 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 from modlamp.core import BaseDescriptor
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2 from modlamp.descriptors import PeptideDescriptor
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3 import pandas as pd
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4 import argparse, os
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6 parser = argparse.ArgumentParser()
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8 parser.add_argument("-I", "--InFile", required=True, default=None, help="Input file")
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9 parser.add_argument("-O", "--OutFile", required=True, default=None, help="Output file")
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10 parser.add_argument("-N", "--Ngrams", required=True, default=None, help="ngrams")
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12 args = parser.parse_args()
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14 file = open(args.InFile)
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15 lines = file.readlines()
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17 Index = []
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18 Pep = []
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21 for line in lines:
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22 if '>' in line:
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23 Index.append(line.strip('\n'))
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24 else:
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25 line = line.strip('\n')
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26 line = line.strip('\r')
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27 Pep.append(line)
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29 df = pd.DataFrame()
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31 for i, l in enumerate(Pep):
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33 D = PeptideDescriptor(l)
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34 D.count_ngrams([int(args.Ngrams)])
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36 df1 = pd.DataFrame(D.descriptor, index=["sequence"+str(i),])
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37 df = pd.concat([df, df1], axis=0)
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39 df = df.fillna(0)
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40 df.to_csv(args.OutFile, sep='\t', index=None)
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