Mercurial > repos > devteam > merge_cols
comparison mergeCols.py @ 0:11de536c87b1 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
| author | devteam |
|---|---|
| date | Mon, 09 Nov 2015 11:45:18 -0500 |
| parents | |
| children | 26d0d9bdbafc |
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| -1:000000000000 | 0:11de536c87b1 |
|---|---|
| 1 import sys, re | |
| 2 | |
| 3 def stop_err( msg ): | |
| 4 sys.stderr.write( msg ) | |
| 5 sys.exit() | |
| 6 | |
| 7 def __main__(): | |
| 8 try: | |
| 9 infile = open ( sys.argv[1], 'r') | |
| 10 outfile = open ( sys.argv[2], 'w') | |
| 11 except: | |
| 12 stop_err( 'Cannot open or create a file\n' ) | |
| 13 | |
| 14 if len( sys.argv ) < 4: | |
| 15 stop_err( 'No columns to merge' ) | |
| 16 else: | |
| 17 cols = sys.argv[3:] | |
| 18 | |
| 19 skipped_lines = 0 | |
| 20 | |
| 21 for line in infile: | |
| 22 line = line.rstrip( '\r\n' ) | |
| 23 if line and not line.startswith( '#' ): | |
| 24 fields = line.split( '\t' ) | |
| 25 line += '\t' | |
| 26 for col in cols: | |
| 27 try: | |
| 28 line += fields[ int( col ) -1 ] | |
| 29 except: | |
| 30 skipped_lines += 1 | |
| 31 | |
| 32 print >>outfile, line | |
| 33 | |
| 34 if skipped_lines > 0: | |
| 35 print 'Skipped %d invalid lines' % skipped_lines | |
| 36 | |
| 37 if __name__ == "__main__" : __main__() |