Mercurial > repos > devteam > merge_cols
annotate mergeCols.py @ 0:11de536c87b1 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author | devteam |
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date | Mon, 09 Nov 2015 11:45:18 -0500 |
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children | 26d0d9bdbafc |
rev | line source |
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0
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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1 import sys, re |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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2 |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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3 def stop_err( msg ): |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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4 sys.stderr.write( msg ) |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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5 sys.exit() |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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6 |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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7 def __main__(): |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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8 try: |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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9 infile = open ( sys.argv[1], 'r') |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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10 outfile = open ( sys.argv[2], 'w') |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
11 except: |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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12 stop_err( 'Cannot open or create a file\n' ) |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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13 |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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14 if len( sys.argv ) < 4: |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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15 stop_err( 'No columns to merge' ) |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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16 else: |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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17 cols = sys.argv[3:] |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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18 |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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19 skipped_lines = 0 |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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20 |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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21 for line in infile: |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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22 line = line.rstrip( '\r\n' ) |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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23 if line and not line.startswith( '#' ): |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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24 fields = line.split( '\t' ) |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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25 line += '\t' |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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26 for col in cols: |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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27 try: |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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28 line += fields[ int( col ) -1 ] |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
29 except: |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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30 skipped_lines += 1 |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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31 |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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32 print >>outfile, line |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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33 |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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34 if skipped_lines > 0: |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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35 print 'Skipped %d invalid lines' % skipped_lines |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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36 |
11de536c87b1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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37 if __name__ == "__main__" : __main__() |