Version 1.3

README.md

@@ -1,6 +1,6 @@
 ## SpliceAI: A deep learning-based tool to identify splice variants
 [![Downloads](https://pepy.tech/badge/spliceai)](https://pepy.tech/project/spliceai)
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-red.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 This package annotates genetic variants with their predicted effect on splicing, as described in [Jaganathan *et al*, Cell 2019 in press](https://doi.org/10.1016/j.cell.2018.12.015).
 
@@ -39,7 +39,7 @@ Required parameters:
 
 Optional parameters:
  - ```-D```: Maximum distance between the variant and gained/lost splice site (default: 50).
- - ```-M```: Mask scores representing annotated acceptor/donor gain and unannotated acceptor/donor loss (default: False).
+ - ```-M```: Mask scores representing annotated acceptor/donor gain and unannotated acceptor/donor loss (default: 0).
 
 Details of SpliceAI INFO field:
 

spliceai/__main__.py

@@ -25,12 +25,14 @@ def get_options():
                         help='"grch37" (GENCODE V24lift37 canonical annotation file in '
                              'package), "grch38" (GENCODE V24 canonical annotation file in '
                              'package), or path to a similar custom gene annotation file')
-    parser.add_argument('-D', metavar='distance', nargs='?', default=50, type=int,
+    parser.add_argument('-D', metavar='distance', nargs='?', default=50,
+                        type=int, choices=range(0, 5000),
                         help='maximum distance between the variant and gained/lost splice '
                              'site, defaults to 50')
-    parser.add_argument('-M', metavar='mask', nargs='?', default=False, type=bool,
+    parser.add_argument('-M', metavar='mask', nargs='?', default=0,
+                        type=int, choices=[0, 1],
                         help='mask scores representing annotated acceptor/donor gain and '
-                             'unannotated acceptor/donor loss, defaults to False')
+                             'unannotated acceptor/donor loss, defaults to 0')
     args = parser.parse_args()
 
     return args

spliceai/utils.py

@@ -28,7 +28,7 @@ def __init__(self, ref_fasta, annotations):
             self.exon_ends = [np.asarray(list(map(int, re.split(',', c)[:-1])))
                               for c in df['EXON_END'].get_values()]
         except IOError as e:
-            logging.error('Error reading gene annotation file {}: {}'.format(annotations, e))
+            logging.error('{}'.format(e))
             exit()
         except (KeyError, pd.errors.ParserError) as e:
             logging.error('Gene annotation file {} not formatted properly: {}'.format(annotations, e))
@@ -37,7 +37,7 @@ def __init__(self, ref_fasta, annotations):
         try:
             self.ref_fasta = Fasta(ref_fasta, rebuild=False)
         except IOError as e:
-            logging.error('Error reading reference genome fasta file {}: {}'.format(ref_fasta, e))
+            logging.error('{}'.format(e))
             exit()
 
         paths = ('models/spliceai{}.h5'.format(x) for x in range(1, 6))