Mercurial > repos > greg > fasta_extract
comparison fasta_extract.py @ 1:3fb7f36c2c8a draft
Uploaded
| author | greg |
|---|---|
| date | Sun, 10 Jan 2016 13:52:36 -0500 |
| parents | bc3f2a5c7b53 |
| children | 79167132946d |
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| 0:bc3f2a5c7b53 | 1:3fb7f36c2c8a |
|---|---|
| 29 sys.stderr.write(msg) | 29 sys.stderr.write(msg) |
| 30 sys.exit(1) | 30 sys.exit(1) |
| 31 | 31 |
| 32 | 32 |
| 33 parser = argparse.ArgumentParser() | 33 parser = argparse.ArgumentParser() |
| 34 parser.add_argument('--input', dest='inputs', action='append', nargs=2, help="Input datasets") | |
| 34 parser.add_argument('--genome_file', dest='genome_file', help='Reference genome fasta index file.') | 35 parser.add_argument('--genome_file', dest='genome_file', help='Reference genome fasta index file.') |
| 35 parser.add_argument('--subtract_from_start', dest='subtract_from_start', type=int, help='Distance to subtract from start.') | 36 parser.add_argument('--subtract_from_start', dest='subtract_from_start', type=int, help='Distance to subtract from start.') |
| 36 parser.add_argument('--add_to_end', dest='add_to_end', type=int, help='Distance to add to end.') | 37 parser.add_argument('--add_to_end', dest='add_to_end', type=int, help='Distance to add to end.') |
| 37 parser.add_argument('--extend_existing', dest='extend_existing', help='Extend existing start/end rather or from computed midpoint.') | 38 parser.add_argument('--extend_existing', dest='extend_existing', help='Extend existing start/end rather or from computed midpoint.') |
| 38 parser.add_argument('--strand', dest='strand', help='Consider strandedness: reverse complement extracted sequence on reverse strand.') | 39 parser.add_argument('--strand', dest='strand', help='Consider strandedness: reverse complement extracted sequence on reverse strand.') |