def test_substitute_config_region_InvalidParameterError(self):
"""
Test whether a InvalidPrama Error is correctly raised
"""
tmp = tempfile.NamedTemporaryFile(delete=False)
tmp.write(self.config_file)
tmp.close()
kwargs = {"config": tmp.name, "region": "123.1231"}
self.assertRaises(InvalidParameterError, substitute_config, **kwargs)
os.unlink(tmp.name)
def test_substitute_config_bitscore_not_numerical(self):
"""
Test whether a InvalidPrama Error is correctly raised
"""
tmp = tempfile.NamedTemporaryFile(delete=False)
tmp.write(self.config_file)
tmp.close()
kwargs = {"config": tmp.name, "bitscores": "one"}
self.assertRaises(InvalidParameterError, substitute_config, **kwargs)
os.unlink(tmp.name)
def test_substitute_config_existing_db(self):
"""
Test whether a InvalidPrama Error is correctly raised
"""
tmp = tempfile.NamedTemporaryFile(delete=False)
tmp.write(self.config_file)
tmp.close()
kwargs = {"config": tmp.name, "database": "uniprot"}
res = substitute_config(**kwargs)
self.assertEqual("uniprot", res["align"]["database"])
os.unlink(tmp.name)
def test_substitute_config_stages(self):
"""
Test whether a InvalidPrama Error is correctly raised
"""
tmp = tempfile.NamedTemporaryFile(delete=False)
tmp.write(self.config_file)
tmp.close()
kwargs = {"config": tmp.name, "stages": "test"}
res = substitute_config(**kwargs)
self.assertEqual(["test"], res["stages"])
os.unlink(tmp.name)
def test_substitute_config_region(self):
"""
Test whether a region is correctly substituted
"""
tmp = tempfile.NamedTemporaryFile(delete=False)
tmp.write(self.config_file)
tmp.close()
kwargs = {"config": tmp.name, "region": "1-10"}
res = substitute_config(**kwargs)
self.assertEqual([1, 10], res["global"]["region"])
os.unlink(tmp.name)
def test_substitute_config_alignment(self):
"""
Test whether a InvalidPrama Error is correctly raised
"""
tmp = tempfile.NamedTemporaryFile(delete=False)
tmp.write(self.config_file)
tmp.close()
kwargs = {"config": tmp.name, "alignment": "test.fasta"}
res = substitute_config(**kwargs)
self.assertEqual("existing", res["align"]["protocol"])
os.unlink(tmp.name)
def test_substitute_config_multiple_bitscore(self):
"""
Test whether a InvalidPrama Error is correctly raised
"""
tmp = tempfile.NamedTemporaryFile(delete=False)
tmp.write(self.config_file)
tmp.close()
kwargs = {"config": tmp.name, "bitscores": "1.0,0.7"}
res = substitute_config(**kwargs)
self.assertTrue("batch" in res)
os.unlink(tmp.name)
def test_unroll_config_batch(self):
"""
test whether config is not unrolled if batch is not defined
"""
tmp = tempfile.NamedTemporaryFile(delete=False)
tmp.write(self.config_file)
tmp.close()
kwargs = {"config": tmp.name, "bitscores": "1.0,0.7"}
res = substitute_config(**kwargs)
res = unroll_config(res)
self.assertTrue(len(res) == 2)
os.unlink(tmp.name)
def test_substitute_config_single_bitscore(self):
"""
Test whether a InvalidPrama Error is correctly raised
"""
tmp = tempfile.NamedTemporaryFile(delete=False)
tmp.write(self.config_file)
tmp.close()
kwargs = {"config": tmp.name, "bitscores": "1.0"}
res = substitute_config(**kwargs)
self.assertEqual(1.0, res["align"]["use_bitscores"])
self.assertEqual(1.0, res["align"]["domain_threshold"])
os.unlink(tmp.name)
