def test_bad_partitions(self):
with TemporaryDirectory(change=True):
for i in [-10, -1, 0]:
with self.assertRaisesRegex(ValueError, "Partitions must be greater than 0"):
core.write_fastas_with_all_genes(self.clusters, "test", partitions=i)
for i in ["str", None, 1.5]:
with self.assertRaisesRegex(TypeError, "Partitions must be an int greater than 0"):
core.write_fastas_with_all_genes(self.clusters, "test", partitions=i)
def test_single_partition(self):
self.dummy_cluster.cds_children = [DummyCDS(1, 3)] * 3
with TemporaryDirectory(change=True):
files = core.write_fastas_with_all_genes(self.clusters, "test.fasta", partitions=1)
assert files == ["test.fasta"]
assert os.path.exists("test.fasta")
expected = "".join(">L{0}\nS{0}\n".format(i) for i in range(len(self.clusters)*3))
assert open("test.fasta").read() == expected
def test_single_file(self):
self.add_cdses_to_region([DummyCDS(1, i) for i in range(3, 6)])
with TemporaryDirectory(change=True):
files = core.write_fastas_with_all_genes(self.regions,
"test.fasta")
assert files == ["test.fasta"]
assert os.path.exists("test.fasta")
expected = "".join(">L{0}\nS{0}\n".format(i)
for i in range(len(self.regions) * 3))
assert open("test.fasta").read() == expected
def test_multiple_files(self):
self.dummy_cluster.cds_children = [DummyCDS(1, 3)] * 3
for partitions in [2, 3]:
with TemporaryDirectory(change=True):
self.index = 0
chunk_size = (len(self.clusters) * 3) // partitions
files = core.write_fastas_with_all_genes(self.clusters, "test.fasta", partitions=partitions)
assert files == ["test%d.fasta" % i for i in range(partitions)]
for index in range(partitions):
assert os.path.exists("test%d.fasta" % index)
print(index, chunk_size)
contents = open("test%d.fasta" % index).read()
assert contents.count(">") == chunk_size
expected = "".join(">L{0}\nS{0}\n".format(i + index * chunk_size) for i in range(chunk_size))
assert contents == expected
def test_empty(self):
with TemporaryDirectory(change=True):
with self.assertRaisesRegex(
ValueError, "Diamond search space contains no sequences"):
core.write_fastas_with_all_genes(self.regions, "test")
