Mercurial > repos > greg > meme_fimo
changeset 5:e85346ab5054 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 16 Jun 2016 08:07:03 -0400 |
| parents | 1f221102ac4d |
| children | 4df8e9f58a53 |
| files | fimo_wrapper.py |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- 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')