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comparison fimo_wrapper.py @ 6:cdcc4bb60bc3 draft

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author iuc
date Wed, 29 Jun 2016 08:35:04 -0400
parents eca84de658b0
children 40b8472e91ca
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5:eca84de658b0 6:cdcc4bb60bc3
54 parser.add_argument('--alpha', dest='alpha', type=float, default=1.0, help='The alpha parameter for calculating position specific priors') 54 parser.add_argument('--alpha', dest='alpha', type=float, default=1.0, help='The alpha parameter for calculating position specific priors')
55 parser.add_argument('--bgfile', dest='bgfile', default=None, help='Background file type, used only if not "default"') 55 parser.add_argument('--bgfile', dest='bgfile', default=None, help='Background file type, used only if not "default"')
56 parser.add_argument('--max_strand', action='store_true', help='If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score') 56 parser.add_argument('--max_strand', action='store_true', help='If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score')
57 parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store') 57 parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store')
58 parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id') 58 parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id')
59 parser.add_argument('--output_separate_motifs', default="no", help='Output one dataset per motif') 59 parser.add_argument('--output_separate_motifs', dest='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', default='no', help='Check each sequence header for UCSC style genomic coordinates') 64 parser.add_argument('--parse_genomic_coord', dest='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', dest='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')
70 parser.add_argument('--interval_output', dest='interval_output', help='Interval output file') 70 parser.add_argument('--interval_output', dest='interval_output', help='Interval output file')