From 56152c3002b37be99f6a8d4669942a3f655da778 Mon Sep 17 00:00:00 2001 From: ashuaibi7 Date: Tue, 19 Nov 2024 08:06:09 -0500 Subject: [PATCH] added new subparser for functionality with running DIALECT to identify interactions --- src/dialect/utils/argument_parser.py | 26 ++++++++++++++++++++------ 1 file changed, 20 insertions(+), 6 deletions(-) diff --git a/src/dialect/utils/argument_parser.py b/src/dialect/utils/argument_parser.py index c46fedc..22340ce 100644 --- a/src/dialect/utils/argument_parser.py +++ b/src/dialect/utils/argument_parser.py @@ -26,12 +26,26 @@ def build_argument_parser(): help="Reference genome (default: hg19)", ) - # # Subparser for DIALECT analysis - # analyze_parser = subparsers.add_parser("analyze", help="Run DIALECT analysis") - # analyze_parser.add_argument("cnt_mtx_fn", help="Path to the count matrix file") - # analyze_parser.add_argument("bmr_fn", help="Path to the BMR file") - # analyze_parser.add_argument("dout", help="Path to the output directory") - # analyze_parser.add_argument("--top_k", default=100, type=int) + # Subparser for DIALECT analysis + identify_parser = subparsers.add_parser( + "identify", help="Run DIALECT to identify interactions" + ) + identify_parser.add_argument( + "-m", "--maf", required=True, help="Path to the input MAF file" + ) + identify_parser.add_argument( + "-b", "--bmr", required=True, help="Path to the BMR file" + ) + identify_parser.add_argument( + "-o", "--out", required=True, help="Path to the output directory" + ) + identify_parser.add_argument( + "-k", + "--top_k", + default=100, + type=int, + help="Number of genes to consider (default: 100 genes with highest mutation count)", + ) # # Subparser for comparison analysis # compare_parser = subparsers.add_parser("compare", help="Run comparison analysis")