def test_invalid_chromosome(self):
message = r"Could not find chromosome .*"
with self.assertRaisesRegex(ValueError, message):
genomes.genome('homo_sapiens',
84,
chromosomes=['ZZZ'],
source='ensembl')
def test_absolute_path(self):
message = r'Directory ".*" does not exist.'
with self.assertRaisesRegex(ValueError, message):
genomes.genome('homo_sapiens',
84,
genome='/invalid/path/genome.fa.gz',
out_dir='/invalid/path/will/raise/error',
source='ensembl')
def test_invalid_out_dir(self):
message = r'Directory ".*" does not exist.'
with self.assertRaisesRegex(ValueError, message):
genomes.genome('homo_sapiens',
84,
genome='genome.fa.gz',
out_dir='/does/not/exist',
source='ensembl')
def test_genome(self):
genomes.genome(
'homo_sapiens', release=84, out_dir=self.tempdir, chromosomes=['MT'], source='ensembl')
self.assertTrue(os.path.isfile(
os.path.join(self.tempdir, 'homo_sapiens.84.chrMT.fa.gz')))
# Confirm that chrom_length file was created!
self.assertTrue(os.path.isfile(
os.path.join(self.tempdir, 'homo_sapiens.84.chrMT.fa.gz.fai')))
def test_genome(self):
genomes.genome('human',
release='26',
out_dir=self.tempdir,
source='gencode')
self.assertTrue(
os.path.isfile(os.path.join(self.tempdir, 'human.26.fa.gz')))
# Confirm that chrom_length file was created!
self.assertTrue(
os.path.isfile(os.path.join(self.tempdir, 'human.26.fa.gz.fai')))
def test_genome_invalid_release(self):
message = r'Invalid release number.'
with self.assertRaisesRegex(ValueError, message):
genomes.genome('human', release='1000', source='gencode')
def test_genome_invalid_species(self):
message = r'Invalid species name.'
with self.assertRaisesRegex(ValueError, message):
genomes.genome(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.genome('human', '27', source='invalid_source')
def test_genome_invalid_release(self):
message = r"Release should be a number between \d+ and \d+"
with self.assertRaisesRegex(ValueError, message):
genomes.genome('homo_sapiens', release=1, source='ensembl')
def test_genome_invalid_species(self):
message = r'Invalid species name.'
with self.assertRaisesRegex(ValueError, message):
genomes.genome('invalid_species_name', 84, source='ensembl')