dbe923ef2f7f3bebed34475ab495e9b6a0746c21,cnvlib/commands.py,,,#,1538

Before Change

P_export_theta = P_export_subparsers.add_parser("theta",
        help=_cmd_export_theta.__doc__)
P_export_theta.add_argument("tumor_segment",
        help=Tumor-sample segmentation file from CNVkit (.cns).)
P_export_theta.add_argument("normal_reference",
        help=Reference copy number profile (.cnn), or normal-sample bin-level
                log2 copy ratios (.cnr).)
P_export_theta.add_argument("-o", "--output", help="Output file name.")
P_export_theta.set_defaults(func=_cmd_export_theta)


// All else: export any number of .cnr or .cns files

for fmt_key, fmt_descr in (
    ("cdt", "Convert log2 ratios to CDT format. Compatible with Java TreeView."),
    ("jtv", "Convert log2 ratios to Java TreeView"s native format."),
    // Not implemented yet:
    // "multi" (Nexus Copy Number "multi1")
    // "gct" (GenePattern).
):
    def _cmd_export_simple(args):
        sample_ids = list(map(core.fbase, args.filenames))
        rows = export.merge_samples(args.filenames)
        formatter = export.EXPORT_FORMATS[fmt_key]
        outheader, outrows = formatter(sample_ids, rows)
        core.write_tsv(args.output, outrows, colnames=outheader)

    P_export_simple = P_export_subparsers.add_parser(fmt_key, help=fmt_descr)
    P_export_simple.add_argument("filenames", nargs="+",
            help=Log2 copy ratio data file(s) (*.cnr), the output of the
                    "fix" sub-command.)
    P_export_simple.add_argument("-o", "--output", help="Output file name.")
    P_export_simple.set_defaults(func=_cmd_export_simple)


// version ---------------------------------------------------------------------

def print_version(_args):
    Display this program"s version.
    print(__version__)

After Change

    outheader, outrows = export.export_freebayes(args.segments, args)
    core.write_tsv(args.output, outrows, colnames=outheader)

P_export_fb = P_export_subparsers.add_parser("freebayes",
        help=_cmd_export_fb.__doc__)
P_export_fb.add_argument("segments", nargs="+",
        help=Segmented copy ratio data files (*.cns), the output of the
                "segment" sub-command.)
P_export_fb.add_argument("-i", "--sample-id",
        help="Sample name, as FreeBayes should see it.")
// Arguments to drop in favor of "call":
P_export_fb.add_argument("--ploidy", type=int, default=2,
        help="Ploidy of the sample cells. [Default: %(default)d]")
P_export_fb.add_argument("--purity", type=float,
        help="Estimated tumor cell purity or cellularity.")
P_export_fb.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).)
// /
// Argument that could be shared across "export":
P_export_fb.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 gender reference.)
P_export_fb.add_argument("-o", "--output", help="Output file name.")
P_export_fb.set_defaults(func=_cmd_export_fb)


// THetA special case: takes tumor .cns and normal .cnr or reference.cnn

Instances