def main(annotation_file, annotation_type, verbose):
from genmod import logger
from genmod.log import init_log
init_log(logger, loglevel="DEBUG")
print(annotation_file)
gene_trees, exon_trees = parse_annotations(annotation_file, annotation_type)
print(gene_trees.keys())
print(exon_trees.keys())
def cli(context, logfile, verbose):
"""Tool for annotating and analyzing genetic variants in the vcf format.\n
For more information, please run:
genmod COMMAND --help \n
"""
from genmod import logger
from genmod.log import init_log, LEVELS
loglevel = LEVELS.get(min(verbose,2), "WARNING")
init_log(logger, logfile, loglevel)
def read_config(config_file, outfile, loglevel):
"""Parse the config file and print it to the output."""
from genmod import logger
from genmod.log import init_log
init_log(logger, loglevel='DEBUG')
logger.info("Reading Config File: {0}".format(config_file))
config_reader = ConfigParser(config_file)
for plugin in config_reader.plugins:
logger.info("Found plugin:{0}".format(plugin))
logger.info("{0}: {1}".format(
plugin,config_reader.plugins[plugin])
)
for category in config_reader.categories:
logger.info("Category {0}: {1}".format(
category, config_reader.categories[category]
))
from genmod.commands import models_command
from click.testing import CliRunner
ANNOTATED_VCF_FILE = "tests/fixtures/test_vcf_annotated.vcf"
VCF_FILE = "tests/fixtures/test_vcf_regions.vcf"
FAMILY_FILE = "tests/fixtures/recessive_trio.ped"
BAD_FAMILY_FILE = "tests/fixtures/annotate_models/one_ind.ped"
EMPTY_VCF_FILE = "tests/fixtures/empty.vcf"
from genmod import logger
from genmod.log import init_log
init_log(logger, loglevel="INFO")
def test_genmod_annotate_models_no_family():
"""docstring for test_genmod_annotate_models"""
runner = CliRunner()
result = runner.invoke(models_command, [VCF_FILE])
# This should fail since there is no family file
assert result.exit_code == 1
def test_genmod_annotate_models():
"""docstring for test_genmod_annotate_models"""
runner = CliRunner()
result = runner.invoke(models_command, [
VCF_FILE,
'-f',
FAMILY_FILE
]
)
else:
if value < threshold:
keep_variant = True
else:
if not discard:
keep_variant = True
if keep_variant:
logger.debug("Keeping variant")
nr_of_passed_variants += 1
print_variant(variant_line=variant,
outfile=outfile,
mode='vcf',
silent=silent)
else:
logger.debug("Discarding variant")
logger.info("Number of variants in file {0}".format(nr_of_variants))
logger.info(
"Number of variants passing filter {0}".format(nr_of_passed_variants))
logger.info(
"Number of variants filtered {0}".format(nr_of_variants -
nr_of_passed_variants))
if __name__ == '__main__':
from genmod.log import init_log
from genmod import logger
init_log(logger, loglevel="DEBUG")
filter()
else:
if value < threshold:
keep_variant = True
else:
if not discard:
keep_variant = True
if keep_variant:
logger.debug("Keeping variant")
nr_of_passed_variants += 1
print_variant(
variant_line=variant,
outfile=outfile,
mode='vcf',
silent=silent
)
else:
logger.debug("Discarding variant")
logger.info("Number of variants in file {0}".format(nr_of_variants))
logger.info("Number of variants passing filter {0}".format(nr_of_passed_variants))
logger.info("Number of variants filtered {0}".format(
nr_of_variants - nr_of_passed_variants))
if __name__ == '__main__':
from genmod.log import init_log
from genmod import logger
init_log(logger, loglevel="DEBUG")
filter()