def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.addarg_out()
parser.add_argument("--gff",
type=os.path.abspath,
help=("Input GFF3 file. If GFF3 not provided, "
"alignments are assumed to be "
"in-frame coding sequences."))
parser.add_argument("--output-data",
"--outputdata",
choices=['protein', 'codon'],
default="codon",
help=("protein=single data column "
"of protein alleles; "
"codon=four columns with: "
"protein frame1 frame2 frame3"))
parser.add_argument("--filter-annotation",
"--filterannotation",
help=("skip GFF entries with text "
"matching this in their 'Notes' field"))
parser.addarg_linebuffer()
parser.addarg_overwrite()
return parser
def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.add_argument("--mvf",
nargs="*",
type=os.path.abspath,
required=True,
help="One or more mvf files.")
parser.addarg_out()
parser.add_argument(
"--new-contigs",
"--newcontigs",
action="store_true",
help=("By default, contigs are matched between files "
"using their text labels in the header. "
"Use this option to turn matching off and treat "
"each file's contigs as distinct."))
parser.add_argument(
"--newsamples",
action="store_true",
help=("By default, samples are matched between files "
"using their text labels in the header. "
"Use this option to turn matching off and treat "
"each file's sample columns as distinct."))
parser.add_argument(
"--main_header_file",
"--mainheaderfile",
help=("Output file will use same headers as "
"this input file (default=first in list)."))
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.addarg_linebuffer()
parser.addarg_overwrite()
return parser
def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.addarg_out()
parser.add_argument(
"--actions",
nargs='*',
help=("set of actions:args to perform, "
"note these are done in order as listed"))
parser.add_argument("--labels",
action="store_true",
help="use sample labels instead of indices")
parser.add_argument("--test",
help="manually input a line for testing")
parser.add_argument("--test-nchar",
"--textnchar",
type=int,
help="total number of samples for test string")
parser.add_argument(
"--more-help",
"--morehelp",
action="store_true",
help="prints full module list and descriptions")
parser.addarg_linebuffer()
parser.add_argument("--verbose",
action="store_true",
help="report every line (for debugging)")
parser.addarg_overwrite()
return parser
def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.add_argument(
"--maf",
help="input MAF file",
required=True,
type=os.path.abspath,
)
parser.add_argument("--out",
help="output MVF file",
type=os.path.abspath,
required=True)
parser.add_argument("--ref-tag",
"--reftag",
help="old reference tag")
parser.add_argument(
"--mvf-ref-label",
"--mvfreflabel",
default="REF",
help=("new label for reference sample (default='REF')"))
parser.add_argument(
"--sample-tags",
"--sampletags",
nargs="*",
required=True,
help=("one or more TAG:NEWLABEL or TAG, items, "
"if TAG found in sample label, replace with "
"NEW (or TAG if NEW not specified) "
"NEW and TAG must each be unique."))
parser.addarg_linebuffer()
parser.addarg_overwrite()
return parser
def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.addarg_out()
parser.add_argument("--gff",
type=os.path.abspath,
help=("Input GFF3 file. If GFF3 not provided, "
"alignments are assumed to be "
"in-frame coding sequences."))
parser.add_argument("--output-data",
"--outputdata",
choices=['protein', 'codon'],
default="codon",
help=("protein=single data column "
"of protein alleles; "
"codon=four columns with: "
"protein frame1 frame2 frame3"))
parser.add_argument("--filter-annotation",
"--filterannotation",
help=("skip GFF entries with text "
"matching this in their 'Notes' field"))
parser.add_argument("--parent-gene-prefix",
"--parentgeneprefix",
default="gene:",
help=("Parent genes prefix when interpreting"
"GFF files. For GFF3 files, 'gene:' "
"is standard, but for older or custom "
"GFF files this may vary. Use 'none' "
"to make empty."))
parser.addarg_linebuffer()
parser.addarg_overwrite()
parser.add_argument(
"--verbose",
action="store_true",
help="""Output excessive data to screen for debugging""")
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.add_argument("--vcf",
type=os.path.abspath,
help="VCF input file")
parser.add_argument("--out", required=True, help="output MVF file")
parser.add_argument(
"--out-flavor",
"--outflavor",
default="dna",
choices=['dna', 'dnaqual', 'dnaqual-indel', 'dna-indel'],
help=("choose output MVF flavor to include "
"quality scores and/or indels"))
parser.add_argument("--mask-depth",
"--maskdepth",
type=int,
default=1,
help="below this read depth mask with N/n")
parser.add_argument(
"--low-depth",
"--lowdepth",
type=int,
default=3,
help=("below this read depth coverage, "
"convert to lower case set to 0 to disable"))
parser.add_argument(
"--mask-qual",
"--maskqual",
type=int,
default=3,
help=("low quality cutoff, bases replaced by N/- "
"set to 0 to disable"))
parser.add_argument(
"--low-qual",
"--lowqual",
type=int,
default=20,
help=("below this quality convert to lower case "
"set to 0 to disable"))
parser.add_argument(
"--contig-ids",
"--contigids",
nargs='*',
help=("manually specify one or more contig ids "
"as ID;VCFLABE;MVFLABEL, note that "
"VCFLABEL must match EXACTLY the contig string "
"labels in the VCF file"))
parser.add_argument(
"--sample-replace",
"--samplereplace",
nargs="*",
help=("one or more TAG:NEWLABEL or TAG, items, "
"if TAG found in sample label, replace with "
"NEW (or TAG if NEW not specified) "
"NEW and TAG must each be unique"))
parser.add_argument(
"--ref-label",
"--reflabel",
default="REF",
help="label for reference sample (default='REF')")
parser.add_argument("--alleles-from",
"--allelesfrom",
default=None,
help="""get additional alignment columns
from INFO fields (:-separated)""")
parser.addarg_linebuffer()
parser.add_argument(
"--no-autoindex",
"--noautoindex",
action="store_true",
help="do not automatically index contigs from the VCF")
parser.add_argument(
"--field-sep",
"--fieldsep",
default="TAB",
choices=['TAB', 'SPACE', 'DBLSPACE', 'COMMA', 'MIXED'],
help="""VCF field separator (default='TAB')""")
parser.add_argument(
"--qual",
action="store_true",
help="""Include Phred genotype quality (GQ) scores""")
parser.addarg_overwrite()
return parser
