Mercurial > repos > greg > meme_fimo

comparison fimo_wrapper.py @ 5:e85346ab5054 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 16 Jun 2016 08:07:03 -0400
parents ce656b846c8e
children 4df8e9f58a53
comparison
equal deleted inserted replaced
4:1f221102ac4d 5:e85346ab5054
59 parser.add_argument('--output_separate_motifs', default="no", help='Output one dataset per motif') 59 parser.add_argument('--output_separate_motifs', default="no", help='Output one dataset per motif')
60 parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix') 60 parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix')
61 parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value') 61 parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value')
62 parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand') 62 parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand')
63 parser.add_argument('--output_path', dest='output_path', help='Output files directory') 63 parser.add_argument('--output_path', dest='output_path', help='Output files directory')
64 parser.add_argument('--parse_genomic_coord', action='store_true', help='Check each sequence header for UCSC style genomic coordinates') 64 parser.add_argument('--parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates')
65 parser.add_argument('--remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates') 65 parser.add_argument('--remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates')
66 parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold') 66 parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold')
67 parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold') 67 parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold')
68 parser.add_argument('--gff_output', dest='gff_output', help='Gff output file') 68 parser.add_argument('--gff_output', dest='gff_output', help='Gff output file')
69 parser.add_argument('--html_output', dest='html_output', help='HTML output file') 69 parser.add_argument('--html_output', dest='html_output', help='HTML output file')
86 fimo_cmd_list.append('--motif-pseudo %4f' % args.motif_pseudo) 86 fimo_cmd_list.append('--motif-pseudo %4f' % args.motif_pseudo)
87 if args.no_qvalue: 87 if args.no_qvalue:
88 fimo_cmd_list.append('--no-qvalue') 88 fimo_cmd_list.append('--no-qvalue')
89 if args.norc: 89 if args.norc:
90 fimo_cmd_list.append('--norc') 90 fimo_cmd_list.append('--norc')
91 if args.parse_genomic_coord: 91 if args.parse_genomic_coord == 'yes':
92 fimo_cmd_list.append('--parse-genomic-coord') 92 fimo_cmd_list.append('--parse-genomic-coord')
93 if args.qv_thresh: 93 if args.qv_thresh:
94 fimo_cmd_list.append('--qv-thresh') 94 fimo_cmd_list.append('--qv-thresh')
95 fimo_cmd_list.append('--thresh %4f' % args.thresh) 95 fimo_cmd_list.append('--thresh %4f' % args.thresh)
96 if args.input_psp is not None: 96 if args.input_psp is not None: