Mercurial > repos > devteam > merge_cols

annotate mergeCols.py @ 1:26d0d9bdbafc 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 14:22:15 +0000
parents 11de536c87b1
children 4576d639d805
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
1 import sys
0
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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2
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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3
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
4 def __main__():
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
5 try:
1
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
6 infile = open(sys.argv[1], 'r')
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
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7 outfile = open(sys.argv[2], 'w')
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
8 except Exception:
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
9 sys.exit('Cannot open or create a file\n')
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
10
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
11 if len(sys.argv) < 4:
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
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12 sys.exit('No columns to merge\n')
0
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
13 else:
1
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
14 cols = sys.argv[3:]
0
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
16 skipped_lines = 0
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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17
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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18 for line in infile:
1
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
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19 line = line.rstrip('\r\n')
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
20 if line and not line.startswith('#'):
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
21 fields = line.split('\t')
0
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
22 line += '\t'
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
23 for col in cols:
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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24 try:
1
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
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25 line += fields[int(col) - 1]
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
26 except Exception:
0
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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27 skipped_lines += 1
1
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
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26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
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29 print(line, file=outfile)
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
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30
0
11de536c87b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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31 if skipped_lines > 0:
1
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
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32 print('Skipped %d invalid lines' % skipped_lines)
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
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33
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
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34
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
35 if __name__ == "__main__":
26d0d9bdbafc "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"
devteam
parents: 0
diff changeset
36 __main__()