def test_extend_parser():
parser = make_rna_reads_arg_parser()
extra_arg_fns = [
add_reference_context_args,
add_protein_sequence_args,
add_variant_sequence_args,
]
for fn in extra_arg_fns:
fn(parser)
args = parser.parse_args([
"--vcf", "ABC.vcf",
"--maf", "ZZZ.maf",
"--variant", "chr1", "39000", "C", "G",
"--bam", "xyz.bam"])
eq_(args.vcf, ["ABC.vcf"])
eq_(args.maf, ["ZZZ.maf"])
eq_(args.variant, [["chr1", "39000", "C", "G"]])
eq_(args.bam, "xyz.bam")
"""
Prints names and sequences of reads supporting a given set of variants.
"""
from __future__ import print_function, division, absolute_import
import logging
import logging.config
import pkg_resources
from isovar.cli.rna_reads import (
variant_reads_dataframe_from_args,
make_rna_reads_arg_parser,
)
logging.config.fileConfig(pkg_resources.resource_filename('isovar.cli', 'logging.conf'))
logger = logging.getLogger(__name__)
parser = make_rna_reads_arg_parser()
parser.add_argument(
"--output",
default="isovar-variant-reads-result.csv",
help="Name of CSV file which contains variant read sequences")
if __name__ == "__main__":
args = parser.parse_args()
logger.info(args)
df = variant_reads_dataframe_from_args(args)
logger.info(df)
df.to_csv(args.output)
