From 8ae5463e3af066f026bbfc8f26b6bbfbf78314ca Mon Sep 17 00:00:00 2001 From: Eric Kofman Date: Tue, 24 Sep 2024 13:06:41 -0700 Subject: [PATCH] bedgraph fix --- marine.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/marine.py b/marine.py index 9ebfd3e..2be3029 100755 --- a/marine.py +++ b/marine.py @@ -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) @@ -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) @@ -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(',')