# HG changeset patch
# User greg
# Date 1466078823 14400
# Node ID e85346ab5054727009e169cf8f738f2a97c5fba2
# Parent  1f221102ac4d0b6d71d9a232177dc98cec164931
Uploaded

diff -r 1f221102ac4d -r e85346ab5054 fimo_wrapper.py
--- a/fimo_wrapper.py	Thu Jun 16 08:06:53 2016 -0400
+++ b/fimo_wrapper.py	Thu Jun 16 08:07:03 2016 -0400
@@ -61,7 +61,7 @@
 parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value')
 parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand')
 parser.add_argument('--output_path', dest='output_path', help='Output files directory')
-parser.add_argument('--parse_genomic_coord', action='store_true', help='Check each sequence header for UCSC style genomic coordinates')
+parser.add_argument('--parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates')
 parser.add_argument('--remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates')
 parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold')
 parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold')
@@ -88,7 +88,7 @@
         fimo_cmd_list.append('--no-qvalue')
     if args.norc:
         fimo_cmd_list.append('--norc')
-    if args.parse_genomic_coord:
+    if args.parse_genomic_coord == 'yes':
         fimo_cmd_list.append('--parse-genomic-coord')
     if args.qv_thresh:
         fimo_cmd_list.append('--qv-thresh')