diff CSP2/bin/screenSNPDiffs.py @ 27:792274118b2e

"planemo upload"
author rliterman
date Wed, 04 Dec 2024 12:50:59 -0500
parents 01431fa12065
children 893a6993efe3
line wrap: on
line diff
--- a/CSP2/bin/screenSNPDiffs.py	Tue Dec 03 16:35:35 2024 -0500
+++ b/CSP2/bin/screenSNPDiffs.py	Wed Dec 04 12:50:59 2024 -0500
@@ -548,17 +548,17 @@
 parser = argparse.ArgumentParser()
 parser.add_argument("--snpdiffs_file", help="Path to the file containing SNP diffs")
 parser.add_argument("--log_dir", help="Path to the log directory")
-parser.add_argument("--min_cov", type=float, help="Minimum coverage")
-parser.add_argument("--min_len", type=int, help="Minimum length")
-parser.add_argument("--min_iden", type=float, help="Minimum identity")
-parser.add_argument("--ref_edge", type=int, help="Reference edge")
-parser.add_argument("--query_edge", type=int, help="Query edge")
-parser.add_argument("--density_windows", help="Density windows (comma-separated)")
-parser.add_argument("--max_snps", help="Maximum SNPs (comma-separated)")
-parser.add_argument("--trim_name", help="Trim name")
+parser.add_argument("--min_cov", default=85, type=float, help="Minimum coverage")
+parser.add_argument("--min_len", default=500,type=int, help="Minimum length")
+parser.add_argument("--min_iden", default=99,type=float, help="Minimum identity")
+parser.add_argument("--ref_edge", default=150,type=int, help="Reference edge")
+parser.add_argument("--query_edge", default=150,type=int, help="Query edge")
+parser.add_argument("--density_windows",default="1000,125,15", help="Density windows (comma-separated)")
+parser.add_argument("--max_snps", default="3,2,1",help="Maximum SNPs (comma-separated)")
+parser.add_argument('--trim_name', type=str, default="", help='trim name')
 parser.add_argument("--output_file", help="Output file")
 parser.add_argument("--ref_id", help="Reference IDs file")
-parser.add_argument("--tmp_dir", help="TMP dir")
+parser.add_argument("--tmp_dir",default="", help="TMP dir")
 
 args = parser.parse_args()