def test_read_observations_without_filtered(self):
"""
Read a file with observations and discard filtered.
"""
with self.fixture.data(DataSourceData) as data:
data_source = DataSource.query.get(
data.DataSourceData.exome_variation_filtered.id)
with data_source.data() as data:
observations = list(tasks.read_observations(data, data_source.filetype,
skip_filtered=True))
assert_equal(observations,
[(26, 'chr20', 76962, 'T', 'C', 'heterozygous', 1),
(27, 'chr20', 126156, 'CAAA', '', 'heterozygous', 1),
(28, 'chr20', 126311, 'CC', '', 'heterozygous', 1),
(30, 'chr20', 131506, 'TCT', '', 'heterozygous', 1),
(31, 'chr20', 131657, 'A', 'G', 'homozygous', 1),
(32, 'chr20', 138004, 'G', 'C', 'homozygous', 1),
(33, 'chr20', 138179, 'C', '', 'heterozygous', 1),
(34, 'chr20', 139362, 'G', 'A', 'homozygous', 1),
(36, 'chr20', 139841, 'A', 'T', 'homozygous', 1),
(37, 'chr20', 139916, '', 'AA', 'homozygous', 1),
(38, 'chr20', 166727, 'G', 'A', 'heterozygous', 1),
(39, 'chr20', 168466, 'T', 'A', 'heterozygous', 1),
(40, 'chr20', 168728, 'T', 'A', 'homozygous', 1),
(41, 'chr20', 168781, 'G', 'T', 'heterozygous', 1)])
def test_read_observations_with_filtered(self):
"""
Read a file with observations and include filtered.
"""
with self.fixture.data(DataSourceData) as data:
data_source = DataSource.query.get(
data.DataSourceData.exome_variation_filtered.id)
with data_source.data() as data:
observations = list(tasks.read_observations(data, data_source.filetype,
skip_filtered=False))
assert_equal(observations,
[(i + 26, 'chr20') + observation for i, observation in
enumerate([(76962, 'T', 'C', 'heterozygous', 1),
(126156, 'CAAA', '', 'heterozygous', 1),
(126311, 'CC', '', 'heterozygous', 1),
(131495, 'T', 'C', 'homozygous', 1),
(131506, 'TCT', '', 'heterozygous', 1),
(131657, 'A', 'G', 'homozygous', 1),
(138004, 'G', 'C', 'homozygous', 1),
(138179, 'C', '', 'heterozygous', 1),
(139362, 'G', 'A', 'homozygous', 1),
(139745, 'T', 'C', 'homozygous', 1),
(139841, 'A', 'T', 'homozygous', 1),
(139916, '', 'AA', 'homozygous', 1),
(166727, 'G', 'A', 'heterozygous', 1),
(168466, 'T', 'A', 'heterozygous', 1),
(168728, 'T', 'A', 'homozygous', 1),
(168781, 'G', 'T', 'heterozygous', 1)])])
def test_read_observations_no_genotypes(self):
"""
Read a file with observations, ignoring genotypes.
"""
with self.fixture.data(DataSourceData) as data:
data_source = DataSource.query.get(
data.DataSourceData.exome_variation.id)
with data_source.data() as data:
observations = list(tasks.read_observations(data, data_source.filetype,
use_genotypes=False))
assert_equal(observations,
[(i + 24 if i < 11 else i + 25, 'chr20') + observation for i, observation in
enumerate([(76962, 'T', 'C', None, 1),
(126156, 'CAAA', '', None, 1),
(126311, 'CC', '', None, 1),
(131495, 'T', 'C', None, 1),
(131506, 'TCT', '', None, 1),
(131657, 'A', 'G', None, 1),
(138004, 'G', 'C', None, 1),
(138179, 'C', '', None, 1),
(139362, 'G', 'A', None, 1),
(139745, 'T', 'C', None, 1),
(139841, 'A', 'T', None, 1),
(166727, 'G', 'A', None, 1),
(168466, 'T', 'A', None, 1),
(168728, 'T', 'A', None, 1),
(168781, 'G', 'T', None, 1)])])
def test_read_observations_gtc(self):
"""
Read a file with observations, using GTC field.
"""
with self.fixture.data(DataSourceData) as data:
data_source = DataSource.query.get(
data.DataSourceData.gonl_summary_variation.id)
with data_source.data() as data:
observations = list(tasks.read_observations(data, data_source.filetype))
assert_equal([o[2:] for o in observations[:15]],
[(60309, 'G', 'T', 'heterozygous', 4),
(60573, 'T', 'C', 'heterozygous', 1),
(60828, 'T', 'G', 'heterozygous', 6),
(61098, 'C', 'T', 'heterozygous', 163),
(61098, 'C', 'T', 'homozygous', 31),
(61270, 'A', 'C', 'heterozygous', 20),
(61682, 'C', 'T', 'heterozygous', 1),
(61795, 'G', 'T', 'heterozygous', 203),
(61795, 'G', 'T', 'homozygous', 64),
(61803, 'A', 'G', 'heterozygous', 1),
(61955, 'C', 'T', 'heterozygous', 1),
(62255, 'T', 'C', 'heterozygous', 4),
(62731, 'C', 'A', 'heterozygous', 93),
(62731, 'C', 'A', 'homozygous', 6),
(63008, 'C', 'A', 'heterozygous', 1)])
def test_read_observations_likelihoods(self):
"""
Read a file with observations and prefer genotype likelihoods.
"""
with self.fixture.data(DataSourceData) as data:
data_source = DataSource.query.get(
data.DataSourceData.exome_variation.id)
with data_source.data() as data:
observations = list(tasks.read_observations(data, data_source.filetype,
prefer_genotype_likelihoods=True))
assert_equal(observations,
[(24, 'chr20', 76962, 'T', 'C', 'heterozygous', 1),
(25, 'chr20', 126156, 'CAAA', '', 'heterozygous', 1),
(26, 'chr20', 126311, 'CC', '', 'homozygous', 1),
(27, 'chr20', 131495, 'T', 'C', 'homozygous', 1),
(28, 'chr20', 131506, 'TCT', '', 'heterozygous', 1),
(29, 'chr20', 131657, 'A', 'G', 'homozygous', 1),
(30, 'chr20', 138004, 'G', 'C', 'homozygous', 1),
(32, 'chr20', 139362, 'G', 'A', 'homozygous', 1),
(33, 'chr20', 139745, 'T', 'C', 'homozygous', 1),
(34, 'chr20', 139841, 'A', 'T', 'homozygous', 1),
(35, 'chr20', 139916, '', 'AA', 'homozygous', 1),
(36, 'chr20', 166727, 'G', 'A', 'heterozygous', 1),
(37, 'chr20', 168466, 'T', 'A', 'heterozygous', 1),
(38, 'chr20', 168728, 'T', 'A', 'homozygous', 1),
(39, 'chr20', 168781, 'G', 'T', 'heterozygous', 1)])