Mercurial > repos > jay > pdaug_peptide_sequence_analysis
annotate PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.py @ 4:b73ba641e514 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
author | jay |
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date | Tue, 12 Jan 2021 18:31:46 +0000 |
parents | e59674e3a391 |
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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1 from modlamp.core import BaseDescriptor |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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2 from modlamp.descriptors import PeptideDescriptor |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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3 import pandas as pd |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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4 import argparse, os |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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6 parser = argparse.ArgumentParser() |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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8 parser.add_argument("-I", "--InFile", required=True, default=None, help="Input file") |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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9 parser.add_argument("-O", "--OutFile", required=True, default=None, help="Output file") |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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10 parser.add_argument("-N", "--Ngrams", required=True, default=None, help="ngrams") |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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12 args = parser.parse_args() |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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14 file = open(args.InFile) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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15 lines = file.readlines() |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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17 Index = [] |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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18 Pep = [] |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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21 for line in lines: |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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22 if '>' in line: |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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23 Index.append(line.strip('\n')) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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24 else: |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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25 line = line.strip('\n') |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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26 line = line.strip('\r') |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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27 Pep.append(line) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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29 df = pd.DataFrame() |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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31 for i, l in enumerate(Pep): |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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33 D = PeptideDescriptor(l) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
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34 D.count_ngrams([int(args.Ngrams)]) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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36 df1 = pd.DataFrame(D.descriptor, index=["sequence"+str(i),]) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
parents:
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37 df = pd.concat([df, df1], axis=0) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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39 df = df.fillna(0) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
jay
parents:
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40 df.to_csv(args.OutFile, sep='\t', index=None) |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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