def test_annotation_invalid_out_dir(self):
message = r"Directory .* does not exist."
with self.assertRaisesRegex(ValueError, message):
genomes.annotation('homo_sapiens',
release=84,
out_dir='/out/dir/that/does/not/exist',
source='ensembl')
def test_annotation(self):
genomes.annotation('homo_sapiens',
release=84,
out_dir=self.tempdir,
annotation=self.tmpfile,
source='ensembl')
self.assertTrue(
os.path.isfile(os.path.join(self.tempdir, self.tmpfile)))
def test_annotation(self):
genomes.annotation('mouse',
release='M15',
out_dir=self.tempdir,
annotation=self.tmpfile,
source='gencode')
self.assertTrue(
os.path.isfile(os.path.join(self.tempdir, self.tmpfile)))
def test_annotation_invalid_release(self):
message = r"Invalid release number."
with self.assertRaisesRegex(ValueError, message):
genomes.annotation('human', release='42000', source='gencode')
def test_annotation_invalid_species(self):
message = r'Invalid species name.'
with self.assertRaisesRegex(ValueError, message):
genomes.annotation(species='invalid_species_name', release='26', source='gencode')
def test_bad_source(self):
message = r'Source .* is not supported.'
with self.assertRaisesRegex(ValueError, message):
genomes.annotation('human', '27', source='invalid_source')
def test_annotation_invalid_release(self):
message = r"Release should be a number between \d+ and \d+"
with self.assertRaisesRegex(ValueError, message):
genomes.annotation('homo_sapiens', 1, source='ensembl')
def test_annotation_invalid_species(self):
message = r'Invalid species name.'
with self.assertRaisesRegex(ValueError, message):
genomes.annotation('invalid_species_name', 84, source='ensembl')