Commit 468aed31 authored by Holly Ruess's avatar Holly Ruess

Merge branch '31-BlacklistRegions' of...

Merge branch '31-BlacklistRegions' of git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis into 31-BlacklistRegions
parents b45e8a00 5e608f93
Pipeline #7088 passed with stages
in 553 minutes and 27 seconds
......@@ -40,7 +40,8 @@ def get_args():
parser.add_argument('-b', '--blacklist',
help="Bed file of blacklisted regions to remove",
required=False)
required=False,
default="None")
args = parser.parse_args()
return args
......@@ -198,7 +199,7 @@ def main():
args = get_args()
design = args.design
files = args.files
blacklist = args.files
blacklist = args.blacklist
# Create a file handler
handler = logging.FileHandler('consensus_peaks.log')
......@@ -230,7 +231,7 @@ def main():
design_diff.to_csv("design_exQC.tsv", header=True, sep='\t', index=False)
# Remove blacklist regions; if blacklist = True
if blacklist:
if os.path.exists(blacklist):
for experiment, df_experiment in design_peaks_df.groupby('experiment_id'):
bl_peaks = blacklist_peaks(experiment, blacklist)
......
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