def test_allele_count_dataframe(): variant = Variant("test_contig", 50, "C", "G") reads = [ AlleleRead(prefix="AAA", allele="C", suffix="TTT", name="C1"), AlleleRead(prefix="AAC", allele="C", suffix="TTA", name="C2"), AlleleRead(prefix="AAA", allele="G", suffix="TTT", name="G1"), ] df = allele_counts_dataframe([(variant, reads)]) assert len(df) == 1, "Wrong number of rows in DataFrame: %s" % (df,) row = df.iloc[0] eq_(row.n_ref, 2) eq_(row.n_alt, 1) eq_(row.n_other, 0)
def test_allele_count_dataframe(): variant = Variant("test_contig", 50, "C", "G") reads = [ AlleleRead(prefix="AAA", allele="C", suffix="TTT", name="C1"), AlleleRead(prefix="AAC", allele="C", suffix="TTA", name="C2"), AlleleRead(prefix="AAA", allele="G", suffix="TTT", name="G1"), ] df = allele_counts_dataframe([(variant, reads)]) assert len(df) == 1, "Wrong number of rows in DataFrame: %s" % (df, ) row = df.iloc[0] eq_(row.n_ref, 2) eq_(row.n_alt, 1) eq_(row.n_other, 0)
Prints number of reads supporting ref, alt, and other alleles at variant loci. """ from __future__ import division, absolute_import import logging import logging.config import pkg_resources from isovar.cli.rna_reads import (make_rna_reads_arg_parser, allele_reads_generator_from_args) from isovar.allele_counts import allele_counts_dataframe 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-allele-counts-result.csv", help="Name of CSV file which contains read sequences") if __name__ == "__main__": args = parser.parse_args() logger.info(args) variants_and_allele_reads_generator = allele_reads_generator_from_args( args) allele_counts_df = allele_counts_dataframe( variants_and_allele_reads_generator) logger.info(allele_counts_df) allele_counts_df.to_csv(args.output)
""" from __future__ import division, absolute_import import logging import logging.config import pkg_resources from isovar.cli.rna_reads import ( make_rna_reads_arg_parser, allele_reads_generator_from_args ) from isovar.allele_counts import allele_counts_dataframe 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-allele-counts-result.csv", help="Name of CSV file which contains read sequences") if __name__ == "__main__": args = parser.parse_args() logger.info(args) variants_and_allele_reads_generator = allele_reads_generator_from_args(args) allele_counts_df = allele_counts_dataframe(variants_and_allele_reads_generator) logger.info(allele_counts_df) allele_counts_df.to_csv(args.output)