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bedgraph fix #44

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merged 1 commit into from
Sep 24, 2024
Merged

bedgraph fix #44

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8 changes: 4 additions & 4 deletions marine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -574,7 +574,7 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in

parser.add_argument('--sailor', type=str, nargs='?', const='CT', default=None, dest='sailor')

parser.add_argument('--bedgraphs', type=str, default=None, help='Conversions for which to output a bedgraph for non-single cell runs, e.g. CT, AI')
parser.add_argument('--bedgraphs', type=str, nargs='?', const='CT', default=None, help='Conversions for which to output a bedgraph for non-single cell runs, e.g. CT, AI')
parser.add_argument('--verbose', dest='verbose', action='store_true')
parser.add_argument('--keep_intermediate_files', dest='keep_intermediate_files', action='store_true')
parser.add_argument('--num_per_sublist', dest='num_per_sublist', type=int, default=6)
Expand Down Expand Up @@ -615,7 +615,7 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in
num_per_sublist = args.num_per_sublist

# Convert bedgraphs argument into list of conversions
if bedgraphs:
if not bedgraphs is None:
if barcode_tag in ['CB', 'IB']:
sys.stderr.write("Can only output bedgraphs for bulk sequencing runs of MARINE")
sys.exit(1)
Expand All @@ -626,9 +626,9 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in
else:
bedgraphs_list = []

if sailor:
if not sailor is None:
if barcode_tag in ['CB', 'IB']:
sys.stderr.write("Can only output bedgraphs for bulk sequencing runs of MARINE")
sys.stderr.write("Can only output sailor for bulk sequencing runs of MARINE")
sys.exit(1)

sailor_list = sailor.upper().replace('I', 'G').split(',')
Expand Down
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