fixed typo issue 165 and None error in regions used

chrombpnet/evaluation/make_bigwigs/bigwig_helper.py

@@ -38,10 +38,10 @@ def get_regions(regions_file, seqlen, regions_used=None):
 
     regions = pd.read_csv(regions_file,sep='\t',header=None)
     #print(regions)
-    if regions_used:
-        regions = [[x[0], int(x[1])+int(x[9])-seqlen//2, int(x[1])+int(x[9])+seqlen//2, int(x[1])+int(x[9])] for x in np.array(regions.values)[regions_used]]
-    else:
+    if regions_used is None:
         regions = [[x[0], int(x[1])+int(x[9])-seqlen//2, int(x[1])+int(x[9])+seqlen//2, int(x[1])+int(x[9])] for x in np.array(regions.values)]
+    else:
+        regions = [[x[0], int(x[1])+int(x[9])-seqlen//2, int(x[1])+int(x[9])+seqlen//2, int(x[1])+int(x[9])] for x in np.array(regions.values)[regions_used]]
 
     return regions
 

chrombpnet/helpers/preprocessing/reads_to_bigwig.py

@@ -18,9 +18,9 @@ def parse_args():
     parser.add_argument('-c', '--chrom-sizes', type=str, required=True, help="Chrom sizes file")
     parser.add_argument('-op', '--output-prefix', type=str, required=True, help="Output prefix (path/to/prefix)")
     parser.add_argument('-d', '--data-type', required=True, type=str, choices=['ATAC', 'DNASE'], help="assay type")
-    parser.add_argumen('--bsort', required=False, default=False, action='store_true', help="use bedtools sort (default is unix sort)")
-    parser.add_argumen('--no-st', required=False,  default=False, action='store_true', help="No streaming in preprocessing")
-    parser.add_argumen('--tmpdir', required=False,  type=str, default=None, help="tmp dir path for unix sort command")
+    parser.add_argument('--bsort', required=False, default=False, action='store_true', help="use bedtools sort (default is unix sort)")
+    parser.add_argument('--no-st', required=False,  default=False, action='store_true', help="No streaming in preprocessing")
+    parser.add_argument('--tmpdir', required=False,  type=str, default=None, help="tmp dir path for unix sort command")
     parser.add_argument('-ps', '--plus-shift', type=int, default=None, help="Plus strand shift applied to reads. Estimated if not specified")
     parser.add_argument('-ms', '--minus-shift', type=int, default=None, help="Minus strand shift applied to reads. Estimated if not specified")
     parser.add_argument('--ATAC-ref-path', type=str, default=None, help="Path to ATAC reference motifs (chrombpnet/data/ATAC.ref.motifs.txt used by default)")

setup.py

@@ -13,7 +13,7 @@
     'include_package_data': True,
     'description': 'chrombpnet predicts chromatin accessibility from sequence',
     'download_url': 'https://github.com/kundajelab/chrombpnet',
-    'version': '0.1.6',
+    'version': '0.1.7',
     'packages': find_packages(),
     'python_requires': '>=3.8',
     'install_requires': install_requires,