Mercurial > repos > rliterman > csp2
comparison CSP2/bin/runSNPPipeline.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 |
|---|---|
| 634 parser = argparse.ArgumentParser(description='CSP2 SNP Pipeline Analysis') | 634 parser = argparse.ArgumentParser(description='CSP2 SNP Pipeline Analysis') |
| 635 parser.add_argument('--reference_id', type=str, help='Reference Isolate') | 635 parser.add_argument('--reference_id', type=str, help='Reference Isolate') |
| 636 parser.add_argument('--output_directory', type=str, help='Output Directory') | 636 parser.add_argument('--output_directory', type=str, help='Output Directory') |
| 637 parser.add_argument('--log_directory', type=str, help='Log Directory') | 637 parser.add_argument('--log_directory', type=str, help='Log Directory') |
| 638 parser.add_argument('--snpdiffs_file', type=str, help='Path to SNPdiffs file') | 638 parser.add_argument('--snpdiffs_file', type=str, help='Path to SNPdiffs file') |
| 639 parser.add_argument('--min_cov', type=float, help='Minimum coverage') | 639 parser.add_argument('--min_cov', default=85,type=float, help='Minimum coverage') |
| 640 parser.add_argument('--min_len', type=int, help='Minimum length') | 640 parser.add_argument('--min_len', default=500,type=int, help='Minimum length') |
| 641 parser.add_argument('--min_iden', type=float, help='Minimum identity') | 641 parser.add_argument('--min_iden', default=99,type=float, help='Minimum identity') |
| 642 parser.add_argument('--ref_edge', type=int, help='Reference edge') | 642 parser.add_argument('--ref_edge', default=150,type=int, help='Reference edge') |
| 643 parser.add_argument('--query_edge', type=int, help='Query edge') | 643 parser.add_argument('--query_edge', default=150,type=int, help='Query edge') |
| 644 parser.add_argument('--density_windows', type=str, help='Density windows') | 644 parser.add_argument('--density_windows', default="1000,125,15",type=str, help='Density windows') |
| 645 parser.add_argument('--max_snps', type=str, help='Maximum SNPs') | 645 parser.add_argument('--max_snps', default="3,2,1", type=str, help='Maximum SNPs') |
| 646 parser.add_argument('--trim_name', type=str, help='Trim name') | 646 parser.add_argument('--trim_name', type=str, default="", help='trim name') |
| 647 parser.add_argument('--max_missing', type=float, help='Maximum missing') | 647 parser.add_argument('--max_missing',default=50, type=float, help='Maximum missing') |
| 648 parser.add_argument('--tmp_dir', type=str, help='Temporary directory') | 648 parser.add_argument('--tmp_dir',default="", type=str, help='Temporary directory') |
| 649 parser.add_argument('--rescue', type=str, help='Rescue edge SNPs (rescue/norescue)') | 649 parser.add_argument('--rescue', default="norescue",type=str, help='Rescue edge SNPs (rescue/norescue)') |
| 650 args = parser.parse_args() | 650 args = parser.parse_args() |
| 651 | 651 |
| 652 reference_id = args.reference_id | 652 reference_id = args.reference_id |
| 653 output_directory = os.path.abspath(args.output_directory) | 653 output_directory = os.path.abspath(args.output_directory) |
| 654 log_directory = os.path.abspath(args.log_directory) | 654 log_directory = os.path.abspath(args.log_directory) |