From 4a2c213d9a9cee615d554fa23664b46184aad968 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 28 Sep 2026 12:30:02 -0500 Subject: Add content-specific CLI options for genotype CSV files. --- scripts/genotypes/preprocess_csv_collect_info.py | 38 ++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'scripts') 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() -- cgit 1.4.1