Python allele_counts_dataframeの例

コード例 #1

ファイル: test_allele_counts.py プロジェクト: Al3n70rn/isovar

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)

コード例 #2

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)

コード例 #3

ファイル: isovar-allele-counts.py プロジェクト: Al3n70rn/isovar

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)

コード例 #4

ファイル: isovar-allele-counts.py プロジェクト: Al3n70rn/isovar

"""

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)