1a84f280b54dd9435da248ecd0cbe8ea2c44b6b4,cnvlib/commands.py,,,#,681

Before Change

P_diagram = AP_subparsers.add_parser("diagram", help=_cmd_diagram.__doc__)
P_diagram.add_argument("filename", nargs="?",
        help=Processed coverage data file (*.cnr), the output of the
                "fix" sub-command.)
P_diagram.add_argument("-s", "--segment",
        help="Segmentation calls (.cns), the output of the "segment" command.")
P_diagram.add_argument("-t", "--threshold", type=float, default=0.5,
        help=Copy number change threshold to label genes.
                [Default: %(default)s])
P_diagram.add_argument("-m", "--min-probes", type=int, default=3,
        help=Minimum number of covered probes to label a gene.
                [Default: %(default)d])
P_diagram.add_argument("-y", "--male-reference", action="store_true",
        help=Assume inputs are already corrected against a male
                reference (i.e. female samples will have +1 log-CNR of
                chrX; otherwise male samples would have -1 chrX).)

After Change

    return tuple(map(float, text.split(",")))


P_call = AP_subparsers.add_parser("call", help=_cmd_call.__doc__)
P_call.add_argument("segment",
        help="Segmentation calls (.cns), the output of the "segment" command.")
P_call.add_argument("-m", "--method",
        choices=("threshold", "clonal"), default="threshold",
        help=Calling method. [Default: %(default)s])
P_call.add_argument("-t", "--thresholds",
        type=csvstring, default="-1.1,-0.3,0.2,0.7",
        help=Hard thresholds for calling each integer copy number, separated
                by commas. Use the "=" sign on the command line, e.g.: -t=-1,0,1
                [Default: %(default)s])
P_call.add_argument("--ploidy", type=int, default=2,
        help="Ploidy of the sample cells. [Default: %(default)d]")
P_call.add_argument("--purity", type=float,
        help="Estimated tumor cell fraction, a.k.a. purity or cellularity.")
P_call.add_argument("-g", "--gender",
        choices=("m", "male", "Male", "f", "female", "Female"),
        help=Specify the sample"s gender as male or female. (Otherwise
                guessed from chrX copy number).)
P_call.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)

Instances