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)