f88d53c3383953d71a70354bcdbf8cfaa37d4a6b,cnvlib/commands.py,,,#,1620

Before Change

        help=Specify the sample"s gender as male or female. (Otherwise
                guessed from chrX copy number).)
// /
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)

After Change

// 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__)

Instances