47f6b481964339b4a7ae8e15f3a3610b9722aeb6,cnvlib/commands.py,,,#,1452

Before Change

P_export_bed = P_export_subparsers.add_parser("bed",
        help=_cmd_export_bed.__doc__)
P_export_bed.add_argument("segments", nargs="+",
        help=Segmented copy ratio data files (*.cns), the output of the
                "segment" or "call" sub-commands.)
P_export_bed.add_argument("-i", "--sample-id", metavar="LABEL",
        help=Identifier to write in the 4th column of the BED file.
                [Default: use the sample ID, taken from the file name])
P_export_bed.add_argument("--ploidy", type=int, default=2,
        help="Ploidy of the sample cells. [Default: %(default)d]")
P_export_bed.add_argument("-x", "--sample-sex", "-g", "--gender",
        dest="sample_sex",
        choices=("m", "y", "male", "Male", "f", "x", "female", "Female"),
        help=Specify the sample"s chromosomal sex as male or female.
                (Otherwise guessed from X and Y coverage).)
P_export_bed.add_argument("--show",
        choices=("ploidy", "variant", "all"), default="ploidy",
        help=Which segmented regions to show:
                "all" = all segment regions;
                "variant" = CNA regions with non-neutral copy number;
                "ploidy" = CNA regions with non-default ploidy.
                [Default: %(default)s])
P_export_bed.add_argument("-y", "--male-reference", action="store_true",
        help=Was a male reference used?  If so, expect half ploidy on
                chrX and chrY; otherwise, only chrY has half ploidy.  In CNVkit,
                if a male reference was used, the "neutral" copy number (ploidy)
                of chrX is 1; chrY is haploid for either reference sex.)
P_export_bed.add_argument("-o", "--output", help="Output file name.")
P_export_bed.set_defaults(func=_cmd_export_bed)

After Change

        nargs="+", metavar="FILES",
        help=Tabular files with Ensembl gene ID and number of reads mapped to
                each gene, from RSEM or another transcript quantifier.)
P_import_rna.add_argument("-f", "--format",
        choices=("rsem", "counts"), default="counts", metavar="NAME",
        help=Input format name: "rsem" for RSEM gene-level read counts
                (*_rsem.genes.results), or "counts" for generic 2-column gene
                IDs and their read counts (e.g. TCGA level 2 RNA expression).
                )
P_import_rna.add_argument("-g", "--gene-resource", metavar="FILE",
        help="Location of gene info table from Ensembl BioMart.")
P_import_rna.add_argument("-c", "--correlations", metavar="FILE",
        help=Correlation of each gene"s copy number with
        expression. Output of cnv_expression_correlate.py.)
P_import_rna.add_argument("-d", "--output-dir",
        default=".", metavar="PATH",
        help=Directory to write a CNVkit .cnr file for each input
                sample. [Default: %(default)s])
P_import_rna.add_argument("-o", "--output", metavar="FILE",
        help="Output file name (summary table).")
P_import_rna.set_defaults(func=_cmd_import_rna)

Instances