def generate_argparser(): """Generate argparse parser """ parser = MvfArgumentParser() parser.addarg_mvf() parser.addarg_out() parser.addarg_sample_indices(nmin=3) parser.addarg_sample_labels(nmin=3) parser.addarg_outgroup_indices() parser.addarg_outgroup_labels() parser.addarg_contig_ids() parser.addarg_contig_labels() return parser
def generate_argparser(): """Generate argparse parser """ pallette = Pallette() parser = MvfArgumentParser() parser.addarg_mvf() parser.add_argument("--out-prefix", "--outprefix", help="Output prefix (not required).") parser.addarg_sample_indices(nmin=3) parser.addarg_sample_labels(nmin=3) parser.addarg_outgroup_indices(nmin=1) parser.addarg_outgroup_labels(nmin=1) parser.addarg_windowsize() parser.add_argument( "--contig-labels", "--contiglabels", nargs=1, help=("Enter the ids of one or more contigs in the " "order they will appear in the chromoplot (as " "comma-separated list)" "(defaults to all ids in order present in MVF)")) parser.add_argument( "--contig-ids", "--contigids", "--contigs", nargs=1, help=("Enter the labels of one or more contigs in the " "order they will appear in the chromoplot (as " "comma-separated list)" "(defaults to all ids in order present in MVF)")) parser.add_argument( "--majority", action="store_true", help=("Plot only 100% shading in the majority track " " rather than shaded proportions in all tracks.")) parser.add_argument( "--info-track", "--infotrack", action="store_true", help=("Include an additional coverage information " "track that will show empty, uninformative, " "and informative loci. (Useful for " "ranscriptomes/RAD or other reduced sampling.")) parser.add_argument("--empty-mask", "--emptymask", choices=pallette.colornames, default="none", help="Mask empty regions with this color.") parser.add_argument( "--yscale", default=20, type=int, help=("Height (in number of pixels) for each track")) parser.add_argument( "--xscale", default=1, type=int, help="Width (in number of pixels) for each window") parser.add_argument("--colors", nargs=3, choices=pallette.colornames, help="three colors to use for chromoplot") parser.add_argument( "--plot-type", "--plottype", choices=["graph", "image"], default="image", help=("PNG image (default) or graph via matplotlib " "(experimental)")) return parser