From 7f496eeaa6d5240756e188f60f1dc6af19e6a25b Mon Sep 17 00:00:00 2001
From: "Akshata N. Rudrapatna"
 <139808049+ANRudrapatna@users.noreply.github.com>
Date: Thu, 19 Mar 2026 17:50:23 -0400
Subject: [PATCH] Update parser.py

Added a new argument ("genome") for the maxATAC average, normalize, predict, benchmark, and prepare functions. This allows users to specify other genomes for e.g., preparation of mm10 ATAC-seq bigWig files and mm10 predictions.

Without this argument, the default behavior of the above functions is to use hg38 genome files for all activities, even when genome files from other builds are specified.
---
 maxatac/utilities/parser.py | 40 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 39 insertions(+), 1 deletion(-)

diff --git a/maxatac/utilities/parser.py b/maxatac/utilities/parser.py
index 840e748..db963b1 100644
--- a/maxatac/utilities/parser.py
+++ b/maxatac/utilities/parser.py
@@ -175,6 +175,14 @@ def get_parser():
                                 default=AUTOSOMAL_CHRS,
                                 help="Chromosomes for averaging. Default: 1-22"
                                 )
+    
+  average_parser.add_argument("--genome",
+                                dest="genome",
+                                type=str,
+                                default="hg38",
+                                required=False,
+                                help="The reference genome build to use."
+                               )
 
     average_parser.add_argument("-o", "--output", "--output_dir",
                                 dest="output_dir",
@@ -223,6 +231,13 @@ def get_parser():
                                 help="Genome sequence 2bit file."
                                 )
 
+    predict_parser.add_argument("--genome",
+                                dest="genome",
+                                type=str,
+                                default="hg38",
+                                required=False,
+                                help="The reference genome build to use.")
+
     predict_parser.add_argument("-i", "-s", "--signal",
                                 dest="signal",
                                 type=str,
@@ -600,9 +615,17 @@ def get_parser():
                                   type=str,
                                   nargs="+",
                                   default=AUTOSOMAL_CHRS,
-                                  help="Chromosomes for normalization. Default: 1-22"
+                                  help="Chromosomes for normalization. Default: 1-22 from the hg38 genome"
                                   )
 
+    normalize_parser.add_argument("--genome",
+                                  dest="genome",
+                                  type=str,
+                                  default="hg38",
+                                  required=False,
+                                  help="The reference genome build to use."
+                                )
+
     normalize_parser.add_argument("-o", "--output", "--output_dir",
                                   dest="output_dir",
                                   type=str,
@@ -722,6 +745,13 @@ def get_parser():
                                         max, mean, min"
                                   )
 
+    benchmark_parser.add_argument("--genome",
+                                  dest="genome",
+                                  type=str,
+                                  default="hg38",
+                                  required=False,
+                                  help="The reference genome build to use.")
+
     benchmark_parser.add_argument("--round_predictions",
                                   dest="round_predictions",
                                   type=int,
@@ -1015,6 +1045,14 @@ def get_parser():
                                 help="The chromosomes to include in the final output."
                                 )
 
+    prepare_parser.add_argument("--genome",
+                                dest="genome",
+                                type=str,
+                                default="hg38",
+                                required=False,
+                                help="The reference genome build to use."
+                                )
+
     prepare_parser.add_argument("-t", "-threads", "--threads",
                                 dest="threads",
                                 type=int,