Mercurial > repos > rliterman > csp2
comparison CSP2/bin/screenSNPDiffs.py @ 27:792274118b2e
"planemo upload"
| author | rliterman |
|---|---|
| date | Wed, 04 Dec 2024 12:50:59 -0500 |
| parents | 01431fa12065 |
| children | 893a6993efe3 |
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| 26:6f85641ecd48 | 27:792274118b2e |
|---|---|
| 546 run_failed = False | 546 run_failed = False |
| 547 | 547 |
| 548 parser = argparse.ArgumentParser() | 548 parser = argparse.ArgumentParser() |
| 549 parser.add_argument("--snpdiffs_file", help="Path to the file containing SNP diffs") | 549 parser.add_argument("--snpdiffs_file", help="Path to the file containing SNP diffs") |
| 550 parser.add_argument("--log_dir", help="Path to the log directory") | 550 parser.add_argument("--log_dir", help="Path to the log directory") |
| 551 parser.add_argument("--min_cov", type=float, help="Minimum coverage") | 551 parser.add_argument("--min_cov", default=85, type=float, help="Minimum coverage") |
| 552 parser.add_argument("--min_len", type=int, help="Minimum length") | 552 parser.add_argument("--min_len", default=500,type=int, help="Minimum length") |
| 553 parser.add_argument("--min_iden", type=float, help="Minimum identity") | 553 parser.add_argument("--min_iden", default=99,type=float, help="Minimum identity") |
| 554 parser.add_argument("--ref_edge", type=int, help="Reference edge") | 554 parser.add_argument("--ref_edge", default=150,type=int, help="Reference edge") |
| 555 parser.add_argument("--query_edge", type=int, help="Query edge") | 555 parser.add_argument("--query_edge", default=150,type=int, help="Query edge") |
| 556 parser.add_argument("--density_windows", help="Density windows (comma-separated)") | 556 parser.add_argument("--density_windows",default="1000,125,15", help="Density windows (comma-separated)") |
| 557 parser.add_argument("--max_snps", help="Maximum SNPs (comma-separated)") | 557 parser.add_argument("--max_snps", default="3,2,1",help="Maximum SNPs (comma-separated)") |
| 558 parser.add_argument("--trim_name", help="Trim name") | 558 parser.add_argument('--trim_name', type=str, default="", help='trim name') |
| 559 parser.add_argument("--output_file", help="Output file") | 559 parser.add_argument("--output_file", help="Output file") |
| 560 parser.add_argument("--ref_id", help="Reference IDs file") | 560 parser.add_argument("--ref_id", help="Reference IDs file") |
| 561 parser.add_argument("--tmp_dir", help="TMP dir") | 561 parser.add_argument("--tmp_dir",default="", help="TMP dir") |
| 562 | 562 |
| 563 args = parser.parse_args() | 563 args = parser.parse_args() |
| 564 | 564 |
| 565 snpdiffs_list = [line.strip() for line in open(args.snpdiffs_file, 'r')] | 565 snpdiffs_list = [line.strip() for line in open(args.snpdiffs_file, 'r')] |
| 566 snpdiffs_list = [line for line in snpdiffs_list if line] | 566 snpdiffs_list = [line for line in snpdiffs_list if line] |