Add content-specific CLI options for genotype CSV files.

1 files changed, 38 insertions, 0 deletions

diff --git a/scripts/genotypes/preprocess_csv_collect_info.py b/scripts/genotypes/preprocess_csv_collect_info.py
index b4b627c..7b0940d 100644
--- a/scripts/genotypes/preprocess_csv_collect_info.py
+++ b/scripts/genotypes/preprocess_csv_collect_info.py
@@ -193,6 +193,44 @@ if __name__ == "__main__":
             type=str,
             default=["-", "NA", "N/A"],
             help="The character indicating a comment line.")
+
+        ## content-specific arguments
+        parser.add_argument(
+            "--markers_field",
+            metavar="MARKERS-FIELD",
+            type=str,
+            default="Locus",
+            help=(
+                "The name of the column (or row, when transposed) containing "
+                "the names of the genetic markers."))
+
+        parser.add_argument(
+            "--chr_field",
+            metavar="CHROMOSOMES-FIELD",
+            type=str,
+            default="Chr",
+            help=(
+                "The name of the column (or row, when transposed) containing "
+                "the names of the names of the chromosomes."))
+
+        parser.add_argument(
+            "--cm_field",
+            metavar="GENETIC-DISTANCES-FIELD",
+            type=str,
+            default="cM",
+            help=(
+                "The name of the column (or row, when transposed) containing "
+                "the genetic distance values in centimorgans."))
+
+        parser.add_argument(
+            "--mb_field",
+            metavar="PHYSICAL-DISTANCES-FIELD",
+            type=str,
+            default="Mb",
+            help=(
+                "The name of the column (or row, when transposed) containing "
+                "the physical distance values in megabase pairs."))
+
         return parser.parse_args()