From 3bd83d2c81e3ac92e05e9e384c7e34b79ce7e32d Mon Sep 17 00:00:00 2001 From: soumyakundu Date: Thu, 6 Jul 2023 16:45:58 -0700 Subject: [PATCH] Added schema for plink without ignored columns --- src/utils/argmanager.py | 2 +- src/utils/helpers.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/src/utils/argmanager.py b/src/utils/argmanager.py index f4e8130..ca845b8 100644 --- a/src/utils/argmanager.py +++ b/src/utils/argmanager.py @@ -37,7 +37,7 @@ def update_variant_summary_args(parser): parser.add_argument("-o", "--out_prefix", type=str, required=True, help="Path to storing the summary file average across folds, directory should already exist") parser.add_argument("-p", "--peaks", type=str, required=True, help="Bed file containing peak regions") parser.add_argument("-g", "--genes", type=str, required=True, help="Bed file containing gene regions") - parser.add_argument("-sc", "--schema", type=str, required=True, choices=['bed', 'plink', 'chrombpnet', 'original'], default='chrombpnet', help="Format for the input variants list") + parser.add_argument("-sc", "--schema", type=str, required=True, choices=['bed', 'plink', 'plink2', 'chrombpnet', 'original'], default='chrombpnet', help="Format for the input variants list") parser.add_argument("-sl", "--score_list", nargs='+', required=True) def fetch_variant_summary_args(): diff --git a/src/utils/helpers.py b/src/utils/helpers.py index d86a571..9d40085 100644 --- a/src/utils/helpers.py +++ b/src/utils/helpers.py @@ -20,6 +20,7 @@ def get_variant_schema(schema): var_SCHEMA = {'original': ['chr', 'pos', 'rsid', 'allele1', 'allele2'], 'plink': ['chr', 'rsid', 'ignore1', 'pos', 'allele1', 'allele2'], + 'plink2': ['chr', 'rsid', 'pos', 'allele1', 'allele2'], 'bed': ['chr', 'pos', 'end', 'allele1', 'allele2', 'rsid'], 'chrombpnet': ['chr', 'pos', 'allele1', 'allele2', 'rsid']} return var_SCHEMA[schema]