def test_predict_gender(): assert predict_gender(x_coverage=10.2, y_coverage=8.1) == 'male' assert predict_gender(x_coverage=20.9, y_coverage=.01) == 'female' # shouldn't raise ``ZeroDivisionError`` assert predict_gender(x_coverage=5.12, y_coverage=0) == 'female' # what does this even mean? assert predict_gender(x_coverage=0, y_coverage=10) == 'unknown'
def test_predict_gender():
assert predict_gender(x_coverage=10.2, y_coverage=8.1) == 'male'
assert predict_gender(x_coverage=20.9, y_coverage=.01) == 'female'
# shouldn't raise ``ZeroDivisionError``
assert predict_gender(x_coverage=5.12, y_coverage=0) == 'female'
# what does this even mean?
assert predict_gender(x_coverage=0, y_coverage=10) == 'unknown'
def sex_checker(self,
group_id=None,
sample_ids=None,
include_coverage=False):
"""Predict gender based on coverage on X/Y chromosomes."""
# limit query on request
query = limit_query(self.sex_chromosome_coverage(),
group=group_id,
samples=sample_ids)
# group tuples (rows) based on first item (sample ID)
samples = itertools.groupby(query, getitem(0))
for sample in samples:
# extract X and Y coverage from the sample group
sample_id, data_group = sample
sex_coverage = [coverage for _, _, coverage in data_group]
# run the predictor
gender = predict_gender(*sex_coverage)
if include_coverage:
# return also raw coverage numbers
yield sample_id, gender, sex_coverage[0], sex_coverage[1]
else:
yield sample_id, gender
def sex_checker(self, group_id=None, sample_ids=None,
include_coverage=False):
"""Predict gender based on coverage on X/Y chromosomes."""
# limit query on request
query = limit_query(self.sex_chromosome_coverage(), group=group_id,
samples=sample_ids)
# group tuples (rows) based on first item (sample ID)
samples = itertools.groupby(query, getitem(0))
for sample in samples:
# extract X and Y coverage from the sample group
sample_id, data_group = sample
sex_coverage = [coverage for _, _, coverage in data_group]
# run the predictor
gender = predict_gender(*sex_coverage)
if include_coverage:
# return also raw coverage numbers
yield sample_id, gender, sex_coverage[0], sex_coverage[1]
else:
yield sample_id, gender
