def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.addarg_out()
parser.addarg_contig_ids()
parser.addarg_contig_labels()
parser.addarg_sample_indices()
parser.addarg_sample_labels()
return parser
def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.addarg_out()
parser.addarg_contig_ids()
parser.addarg_contig_labels()
parser.addarg_sample_indices()
parser.addarg_sample_labels()
parser.addarg_mincoverage()
parser.addarg_windowsize()
parser.add_argument(
"--base-match",
"--basematch",
help="String of bases to match (i.e. numerator).")
parser.add_argument(
"--base-total",
"--basetotal",
help="String of bases for total (i.e. denominator).")
return parser
def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.addarg_out()
parser.addarg_sample_indices()
parser.addarg_sample_labels()
parser.addarg_contig_ids()
parser.addarg_contig_labels()
parser.addarg_windowsize()
parser.add_argument("--raxml-outgroups",
"--raxmloutgroups",
help=("Comma-separated list of outgroup "
"taxon labels to use in RAxML."))
parser.add_argument("--root-with",
"--rootwith",
help=("Comma-separated list of taxon labels "
"to root trees with after RAxML"))
parser.add_argument("--output-contig-labels",
"--outputcontiglabels",
action="store_true",
help=("Output will use contig labels "
"instead of id numbers."))
parser.add_argument("--output-empty",
"--outputempty",
action="store_true",
help=("Include entries of windows "
"with no data in output."))
parser.add_argument(
"--choose-allele",
"--chooseallele",
"--hapmode",
default="none",
dest="choose_allele",
choices=[
"none", "randomone", "randomboth", "major", "minor",
"majorminor"
],
help=("Chooses how heterozygous alleles are "
"handled. (none=no splitting (default); "
"randomone=pick one allele randomly "
"(recommended); randomboth=pick two alleles "
"randomly, but keep both; major=pick the "
"more common allele; minor=pick the less "
"common allele; majorminor= pick the major in "
"'a' and minor in 'b'"))
parser.add_argument("--min-sites",
"--minsites",
type=int,
default=100,
help="minimum number of sites ")
parser.add_argument(
"--min-seq-coverage",
"--minseqcoverage",
type=float,
default=0.1,
help=("proportion of total alignment a sequence"
"must cover to be retianed [0.1]"))
parser.add_argument("--min-depth",
"--mindepth",
type=int,
default=4,
help=("minimum number of alleles per site"))
parser.add_argument(
"--bootstrap",
type=int,
help=("turn on rapid bootstrapping for RAxML and "
"perform specified number of replicates"))
parser.add_argument("--raxml-model",
"--raxmlmodel",
default="GTRGAMMA",
help=("choose RAxML model"))
parser.add_argument("--raxml-path",
"--raxmlpath",
default="raxml",
help="RAxML path for manual specification.")
parser.add_argument(
"--raxml-opts",
"--raxmlopts",
default="",
help=("specify additional RAxML arguments as a "
"double-quotes encased string"))
parser.add_argument(
"--duplicate-seq",
"--duplicateseq",
default="dontuse",
choices=["dontuse", "keep", "remove"],
help=("dontuse=remove duplicate sequences prior to "
"RAxML tree inference, then add them to the "
"tree manually as zero-branch-length sister "
"taxa; keep=keep in for RAxML tree inference "
"(may cause errors for RAxML); "
"remove=remove entirely from alignment"))
parser.add_argument("--temp-dir",
"--tempdir",
default='./raxmltemp',
type=os.path.abspath,
help=("Temporary directory path"))
parser.add_argument("--temp-prefix",
"--tempprefix",
default="mvftree",
help=("Temporary file prefix"))
return parser