From 8d61fa1ca69a91baee4cbc2261575a7a1d26fd3c Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 8 Sep 2020 12:44:08 +0200
Subject: [PATCH] Option to save bed file.
---
create_metagene_profile.py | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/create_metagene_profile.py b/create_metagene_profile.py
index 79c495b..3b185a4 100755
--- a/create_metagene_profile.py
+++ b/create_metagene_profile.py
@@ -72,6 +72,7 @@ import sys
import warnings
from copy import deepcopy
from pathlib import Path
+from shutil import copyfile
from tempfile import NamedTemporaryFile
from collections import defaultdict
# from itertools import chain
@@ -310,6 +311,10 @@ def main():
help="Path to a file containing one gene identifier per line.\n"
"The metagene profile will only take into account those genes.\n"
"This should not be used at the same time as option -c")
+ parser.add_argument(
+ "-k", "--keep_bed",
+ help="Path to a file where bed coordinates of the genes "
+ "listed whith option -g are to be saved.")
parser.add_argument(
"-c", "--bed_coordinates",
help="Path to a file containing the coordinates of the features "
@@ -380,6 +385,9 @@ def main():
args.bigwig_files, bed_filename,
plot_filename=args.profile_plot, **extra_parameters)
if args.gene_list:
+ if args.keep_bed:
+ copyfile(bed_filename, args.keep_bed)
+ print(f"bed coordinates saved in: {args.keep_bed}")
os.unlink(bed_filename)
return 0
--
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