[2] | 1 | import sys, re |
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| 2 | |
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| 3 | def stop_err( msg ): |
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| 4 | sys.stderr.write( msg ) |
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| 5 | sys.exit() |
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| 6 | |
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| 7 | def __main__(): |
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| 8 | try: |
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| 9 | infile = open ( sys.argv[1], 'r') |
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| 10 | outfile = open ( sys.argv[2], 'w') |
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| 11 | except: |
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| 12 | stop_err( 'Cannot open or create a file\n' ) |
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| 13 | |
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| 14 | if len( sys.argv ) < 4: |
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| 15 | stop_err( 'No columns to merge' ) |
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| 16 | else: |
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| 17 | cols = sys.argv[3:] |
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| 18 | |
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| 19 | skipped_lines = 0 |
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| 20 | |
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| 21 | for line in infile: |
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| 22 | line = line.rstrip( '\r\n' ) |
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| 23 | if line and not line.startswith( '#' ): |
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| 24 | fields = line.split( '\t' ) |
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| 25 | line += '\t' |
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| 26 | for col in cols: |
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| 27 | try: |
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| 28 | line += fields[ int( col ) -1 ] |
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| 29 | except: |
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| 30 | skipped_lines += 1 |
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| 31 | |
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| 32 | print >>outfile, line |
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| 33 | |
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| 34 | if skipped_lines > 0: |
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| 35 | print 'Skipped %d invalid lines' % skipped_lines |
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| 36 | |
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| 37 | if __name__ == "__main__" : __main__() |
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