def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.add_argument("--out",
type=os.path.abspath,
help="Output path of FASTA file.",
required=True)
parser.addarg_regions()
parser.addarg_sample_indices()
parser.addarg_sample_labels()
parser.add_argument(
"--label-type",
"--labeltype",
choices=('long', 'short'),
default='long',
help=("Long labels with all metadata or short ids"))
parser.add_argument("--output-data",
"--outputdata",
choices=("dna", "rna", "prot"),
help="Output dna, rna or prot data.")
parser.add_argument(
"--buffer",
type=int,
default=10,
help="size (Mbp) of write buffer for each sample")
parser.add_argument(
"--temp_dir",
"--tempdir",
default=".",
help="directory to write temporary fasta files")
return parser
def generate_argparser():
"""Generate argparse parser
"""
parser = MvfArgumentParser()
parser.addarg_mvf()
parser.add_argument("--out",
type=os.path.abspath,
help="Output Phylip file.",
required=True)
parser.addarg_regions()
parser.add_argument(
"--label-type",
"--labeltype",
choices=('long', 'short'),
default='short',
help="Long labels with all metadata or short ids")
parser.add_argument("--output-data",
"--outputdata",
choices=("dna", "rna", "prot"),
help="Output dna, rna or prot data.")
parser.addarg_sample_indices()
parser.addarg_sample_labels()
parser.add_argument(
"--buffer",
type=int,
default=100000,
help="size (bp) of write buffer for each sample")
parser.add_argument(
"--temp_dir",
"--tempdir",
default=".",
help="directory to write temporary fasta files")
parser.add_argument("--partition",
action="store_true",
help=("Output a CSV partitions file with RAxML"
"formatting for use in partitioned "
"phylogenetic methods."))
return parser
