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
