def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.addarg_out()
parser.addarg_sample_indices(nmin=2)
parser.addarg_sample_labels(nmin=2)
parser.addarg_windowsize()
parser.addarg_mincoverage()
parser.add_argument("--data-type",
"--datatype",
choices=("dna", "prot"),
help=("Data type to compare."
"(This option is only needed for codon "
" MVF files, others will default.)"))
parser.add_argument("--ambig",
choices=("random2", "random3"),
help=("By default, ambiguous nucleotides are "
"excluded. This option will include "
"sets of ambiguous characters by "
"randomly choosing one of the options "
"for: RYMKWS ('random2') or "
"RYMKWS+BDHV ('random3')"))
parser.add_argument(
"--emit-counts",
action="store_true",
help=("output additional file that presents "
"the raw counts of pairwise patterns for "
"each sample pair tested for each window"))
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_windowsize()
parser.addarg_mincoverage()
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_windowsize()
parser.addarg_mincoverage()
parser.add_argument("--output-lists", action="store_true")
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_gff()
parser.addarg_out()
parser.addarg_samples()
parser.addarg_windowsize()
parser.addarg_mincoverage()
parser.add_argument(
"--allele-groups",
"--allelegroups",
nargs='*',
help=("GROUP1:LABEL,LABEL GROUP2:LABEL,LABEL "))
parser.add_argument("--species-groups",
"--speciesgroups",
nargs='*')
parser.add_argument(
"--chi-test",
"--chitest",
help=("Input two number values for expected "
"Nonsynonymous and Synonymous expected values."))
parser.add_argument(
"--target",
nargs="*",
help=("Specify the taxa labels that define the "
"target lineage-specific branch to be tested."))
parser.add_argument("--num-target-species",
"--targetspec",
type=int,
default=1,
help=("Specify the minimum number of "
"taxa in the target set "
"that are required to conduct analysis"))
parser.add_argument("--output-align",
"--outputalign",
help=("Output alignment to this file path in "
"phylip format."))
parser.add_argument(
"--outgroup",
help=("Specify sample name with which to root trees."))
parser.add_argument(
"--use-labels",
"--uselabels",
action="store_true",
help="Use contig labels instead of IDs in output.")
parser.add_argument("--codeml-path",
"--codemlpath",
default="codeml",
type=os.path.abspath,
help="Full path for PAML codeml executable.")
parser.add_argument("--raxml-path",
"--raxmlpath",
type=os.path.abspath,
default="raxml",
help="Full path to RAxML program executable.")
parser.add_argument("--start-contig",
"--startcontig",
type=int,
default=0,
help="Numerical ID for the starting contig.")
parser.add_argument("--end-contig",
"--endcontig",
type=int,
default=100000000,
help="Numerical id for the ending contig.")
parser.add_argument(
"--paml-tmp",
"--pamltmp",
default="pamltmp",
type=os.path.abspath,
help="path for temporary folder for PAML output files")
parser.add_argument(
"--all-sample-trees",
"--allsampletrees",
action="store_true",
help=("Makes trees from all samples instead of "
"only the most complete sequence from "
"each species"))
parser.add_argument(
"--branch-lrt",
"--branchlrt",
type=os.path.abspath,
help=("Specify the output file for and turn on the "
"RAxML-PAML format LRT test scan for "
"selection on the target branch in addition "
"to the basic patterns scan"))
parser.add_argument("--verbose",
action="store_true",
help="additional screen output")
return parser
