def load_coverage(chanjo_db, mip_case, group_id, threshold=None, use_family=False):
"""Load coverage for a case."""
for sample_id, bed_path in mip_case.chanjo_sample_outputs():
if use_family:
sample_id = "{}-{}".format(mip_case.family_id, sample_id)
logger.info("load coverage for %s", sample_id)
if chanjo_db.query(ChanjoSample).filter_by(id=sample_id).first():
raise ChanjoSampleLoadedError(sample_id)
with open(bed_path, "r") as bed_stream:
coverage.load(chanjo_db, bed_stream, source=bed_path, group=group_id, sample=sample_id, threshold=threshold)
def test_load(chanjo_db):
with open('tests/fixtures/coverage/ADM1136A1.bed') as bed_stream:
coverage.load(chanjo_db, bed_stream, group='test-group')
sample_obj = chanjo_db.query(Sample).filter_by(sample_id='ADM1136A1').one()
assert sample_obj.sample_id == 'ADM1136A1'
assert len(sample_obj.exon_stats) == 70 * 6
# test loading the sample samples again
# expect just to work without changed results
with open('tests/fixtures/coverage/ADM1136A1.bed') as bed_stream:
coverage.load(chanjo_db, bed_stream)
assert chanjo_db.samples(group_id='test-group').count() == 1