Added schema for plink without ignored columns

kundajelab · Jul 6, 2023 · 3bd83d2 · 3bd83d2
1 parent 95b600e
commit 3bd83d2
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Showing 2 changed files with 2 additions and 1 deletion.
diff --git 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
@@ -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]