ca456d591851e7087d74ae037f4fdefc31d03828,src/pyscenic/scenic.py,,create_argument_parser,#,249

Before Change

    parser_motifs.add_argument("-n","--nomenclature",
                               type=str, default="HGNC",
                               help="The nomenclature used for the gene signatures.")
    parser_motifs.add_argument("-o", "--output",
                            type=argparse.FileType("w"), default=sys.stdout,
                            help="Output file/stream.")
    add_recovery_parameters(parser_motifs)
    add_annotation_parameters(parser_motifs)
    add_computation_parameters(parser_motifs)
    parser_motifs.set_defaults(func=find_motifs_command)

After Change

    parser_prune.add_argument("-o", "--output",
                            type=argparse.FileType("w"), default=sys.stdout,
                            help="Output file/stream, i.e. a table of enriched motifs and target genes (CSV).")
    parser_prune.add_argument("-n", "--no_pruning", action="store_const", const = "yes",
                              help="Do not perform pruning, i.e. find enriched motifs.")
    add_recovery_parameters(parser_prune)
    add_annotation_parameters(parser_prune)
    add_computation_parameters(parser_prune)
    add_module_parameters(parser_prune)

Instances