Mercurial > repos > devteam > merge_cols

annotate mergeCols.py @ 2:dd40b1e9eebe draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
author devteam
date Wed, 03 Jun 2020 10:22:39 -0400
parents 28ca7552e884
children ae7843d06f8f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
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1 import sys
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3
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4 def __main__():
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5 try:
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dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
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6 infile = open(sys.argv[1], 'r')
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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7 outfile = open(sys.argv[2], 'w')
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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8 except Exception:
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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9 sys.exit('Cannot open or create a file\n')
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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10
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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11 if len(sys.argv) < 4:
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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12 sys.exit('No columns to merge\n')
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13 else:
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dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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14 cols = sys.argv[3:]
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15
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16 skipped_lines = 0
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17
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18 for line in infile:
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dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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parents: 0
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19 line = line.rstrip('\r\n')
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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20 if line and not line.startswith('#'):
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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21 fields = line.split('\t')
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22 line += '\t'
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23 for col in cols:
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24 try:
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dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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25 line += fields[int(col) - 1]
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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26 except Exception:
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27 skipped_lines += 1
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dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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29 print(line, file=outfile)
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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30
0
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31 if skipped_lines > 0:
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dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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32 print('Skipped %d invalid lines' % skipped_lines)
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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35 if __name__ == "__main__":
dd40b1e9eebe "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
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36 __main__()