Mercurial > repos > jjohnson > cummerbund
comparison cuffdiff_wrapper.py @ 13:4597c429b6fb
Return nonzero exit code from cuffdiff_wrapper.py on error
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 17 Jul 2013 07:58:39 -0500 |
| parents | 6a9bc26ab8d9 |
| children | d10befb0867a |
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| 12:e132e60f95b1 | 13:4597c429b6fb |
|---|---|
| 31 | 31 |
| 32 setattr(parser.values, option.dest, labels) | 32 setattr(parser.values, option.dest, labels) |
| 33 | 33 |
| 34 def stop_err( msg ): | 34 def stop_err( msg ): |
| 35 sys.stderr.write( "%s\n" % msg ) | 35 sys.stderr.write( "%s\n" % msg ) |
| 36 sys.exit() | 36 sys.exit(1) |
| 37 | 37 |
| 38 # Copied from sam_to_bam.py: | 38 # Copied from sam_to_bam.py: |
| 39 def check_seq_file( dbkey, cached_seqs_pointer_file ): | 39 def check_seq_file( dbkey, cached_seqs_pointer_file ): |
| 40 seq_path = '' | 40 seq_path = '' |
| 41 for line in open( cached_seqs_pointer_file ): | 41 for line in open( cached_seqs_pointer_file ): |