Mercurial > repos > greg > repmatch_gff3
comparison repmatch_gff3.py @ 6:6df81aade62c draft
Uploaded
| author | greg |
|---|---|
| date | Sat, 28 Nov 2015 14:54:33 -0500 |
| parents | d33030c8e2cc |
| children | 39cb3eeacdbd |
comparison
equal
deleted
inserted
replaced
| 5:53cbf79396d7 | 6:6df81aade62c |
|---|---|
| 18 parser.add_argument('--step', dest='step', type=int, default=0, help='Step size of distance for each iteration') | 18 parser.add_argument('--step', dest='step', type=int, default=0, help='Step size of distance for each iteration') |
| 19 parser.add_argument('--replicates', dest='replicates', type=int, default=2, help='Minimum number of replicates that must be matched for merging to occur') | 19 parser.add_argument('--replicates', dest='replicates', type=int, default=2, help='Minimum number of replicates that must be matched for merging to occur') |
| 20 parser.add_argument('--low_limit', dest='low_limit', type=int, default=-1000, help='Lower limit for c-w distance filter') | 20 parser.add_argument('--low_limit', dest='low_limit', type=int, default=-1000, help='Lower limit for c-w distance filter') |
| 21 parser.add_argument('--up_limit', dest='up_limit', type=int, default=1000, help='Upper limit for c-w distance filter') | 21 parser.add_argument('--up_limit', dest='up_limit', type=int, default=1000, help='Upper limit for c-w distance filter') |
| 22 parser.add_argument('--output_files', dest='output_files', default='simple', help='Restrict output dataset collections.') | 22 parser.add_argument('--output_files', dest='output_files', default='simple', help='Restrict output dataset collections.') |
| 23 parser.add_argument('--plot_format', dest='plot_format', default=None, help='Output format for graph') | |
| 24 parser.add_argument('--output_summary', dest='output_summary', help='Matched groups in gff format') | 23 parser.add_argument('--output_summary', dest='output_summary', help='Matched groups in gff format') |
| 25 parser.add_argument('--output_orphan', dest='output_orphan', default=None, help='Orphans in tabular format') | 24 parser.add_argument('--output_orphan', dest='output_orphan', default=None, help='Orphans in tabular format') |
| 26 parser.add_argument('--output_detail', dest='output_detail', default=None, help='Details in tabular format') | 25 parser.add_argument('--output_detail', dest='output_detail', default=None, help='Details in tabular format') |
| 27 parser.add_argument('--output_key', dest='output_key', default=None, help='Keys in tabular format') | 26 parser.add_argument('--output_key', dest='output_key', default=None, help='Keys in tabular format') |
| 28 parser.add_argument('--output_histogram', dest='output_histogram', default=None, help='Histogram in plot_format') | 27 parser.add_argument('--output_histogram', dest='output_histogram', default=None, help='Histogram') |
| 29 | 28 |
| 30 args = parser.parse_args() | 29 args = parser.parse_args() |
| 31 | 30 |
| 32 dataset_paths = [] | 31 dataset_paths = [] |
| 33 hids = [] | 32 hids = [] |
| 41 args.step, | 40 args.step, |
| 42 args.replicates, | 41 args.replicates, |
| 43 args.up_limit, | 42 args.up_limit, |
| 44 args.low_limit, | 43 args.low_limit, |
| 45 args.output_files, | 44 args.output_files, |
| 46 args.plot_format, | |
| 47 args.output_summary, | 45 args.output_summary, |
| 48 args.output_orphan, | 46 args.output_orphan, |
| 49 args.output_detail, | 47 args.output_detail, |
| 50 args.output_key, | 48 args.output_key, |
| 51 args.output_histogram) | 49 args.output_histogram) |