def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.addarg_out()
parser.addarg_gff()
parser.add_argument("--filter-annotation",
"--filterannotation",
help=("Skip entries in the GFF file that "
"contain this string in their 'Notes'"))
parser.add_argument(
"--nongenic-mode",
"--nongenicmode",
action="store_true",
help=("Instead of returning annotated genes, "
"return the non-genic regions without "
"without changing contigs or coordinates"))
parser.add_argument(
"--nongenic-margin",
"--nongenicmargin",
type=int,
default=0,
help=("for --unnanotated-mode, only retain "
"positions that are this number of bp away "
"from an annotated region boundary"))
parser.addarg_linebuffer()
parser.addarg_overwrite()
return parser
def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.addarg_out()
parser.addarg_gff()
parser.add_argument("--filter-annotation",
"--filterannotation",
help=("Skip entries in the GFF file that "
"contain this string in their 'Notes'"))
parser.add_argument(
"--nongenic-mode",
"--nongenicmode",
action="store_true",
help=("Instead of returning annotated genes, "
"return the non-genic regions without "
"without changing contigs or coordinates"))
parser.add_argument(
"--nongenic-margin",
"--nongenicmargin",
type=int,
default=0,
help=("for --unnanotated-mode, only retain "
"positions that are this number of bp away "
"from an annotated region boundary"))
parser.add_argument("--gene-prefix",
"--geneprefix",
default="mRNA:",
help=("Gene entry prefix when interpreting"
"GFF files. For GFF3 files, 'mRNA:' "
"is standard, but for older or custom "
"GFF files this may vary. Use 'none' "
"to make empty."))
parser.addarg_linebuffer()
parser.addarg_overwrite()
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
