def sex(context, prefix, bam_path):
"""Guess the sex of a BAM alignment."""
try:
result = sex_from_bam(bam_path, prefix=prefix)
except Exception:
logging.exception("Something went really wrong :(")
context.abort()
# print the results to the console for pipeability (csv)
click.echo("#{prefix}X_coverage\t{prefix}Y_coverage\tsex".format(prefix=prefix))
click.echo("\t".join(map(text_type, result)))
def sex(context, prefix, bam_path):
"""Guess the sex of a BAM alignment."""
try:
result = sex_from_bam(bam_path, prefix=prefix)
except Exception:
logging.exception('Something went really wrong :(')
context.abort()
# print the results to the console for pipeability (csv)
click.echo("#{prefix}X_coverage\t{prefix}Y_coverage\tsex"
.format(prefix=prefix))
click.echo('\t'.join(map(text_type, result)))
def test_sex_from_bam():
# use fixtures bam - doesn't have coverage on Y chromosome
result = sex_from_bam('tests/fixtures/ccds.mini.sorted.bam')
assert result.x_coverage > result.y_coverage
assert result.sex == 'female'
def test_sex_from_bam(bam_path):
# use fixtures bam - doesn't have coverage on Y chromosome
result = sex_from_bam(bam_path)
assert result.x_coverage > result.y_coverage
assert result.sex == 'female'
