def test_database_init_wrong_path(self):
with self.assertRaises(FileNotFoundError):
blast.Database(source_dir=self.test_dir /
Path("not_existing_path"),
name="test_db")
blast.Database(source_dir=self.test_dir /
Path("data/blast_query_data/seqs.fasta"),
name="test_db")
def test_aggregate_wrong_dir(self):
with self.assertRaises(FileNotFoundError):
blast.Database(source_dir=Path(""), name="test_db")._aggregate(
self.test_dir / Path("not existing"),
Path("blast_input.fasta"))
blast.Database(source_dir=Path(""), name="test_db")._aggregate(
self.test_dir / Path("data/blast_query_data/seqs.fasta"),
Path("blast_input.fasta"))
def test_clear_files(self):
db, tmp = blast.Database(source_dir=self.test_dir /
Path("data/fasta_test_data"),
name="test_db").create()
db.clear_files()
self.assertFalse((self.test_dir / Path("test_db.nhr")).exists())
self.assertFalse((self.test_dir / Path("test_db.nin")).exists())
self.assertFalse((self.test_dir / Path("test_db.nsq")).exists())
def test_create(self, ):
db, output = blast.Database(source_dir=self.test_dir /
Path("data/fasta_test_data"),
name="test_db").create()
self.assertTrue(Path("test_db.nhr").exists())
self.assertTrue(Path("test_db.nhr").exists())
self.assertTrue(Path("test_db.nsq").exists())
db.clear_files()
def test_repair_ok(self):
db = blast.Database(source_dir=Path(""), name="test_db")
result = db.repair_fasta(self.test_dir /
Path("data/blast_query_data/seqs.fasta"))
expected = """>seqs|1
ATGCTGATCG
>seqs|2
GACGGTACG"""
self.assertEqual(result, expected)
def test_query_wrong_dir(self):
with self.assertRaises(FileNotFoundError):
db = blast.Database(source_dir=self.test_dir /
Path("data/fasta_test_data"),
name="test_db")
db.create()
db.query(self.test_dir / Path("data/blast_query_data/seqs.fasta"),
config={},
blast_format="10 qseqid sseqid score",
headers=tuple())
def test_query_wrong_command(self):
with self.assertRaises(subprocess.SubprocessError):
db = blast.Database(source_dir=self.test_dir /
Path("data/fasta_test_data"),
name="test_db")
db.create()
db.query(self.test_dir / Path("data/fasta_test_data/"),
blast_format="test_wrong_format",
config={"task": "blastn-short"},
headers=tuple())
db.clear_files()
def test_query_wrong_kwargs(self):
with self.assertRaises(ValueError):
db = blast.Database(source_dir=self.test_dir /
Path("data/fasta_test_data"),
name="test_db")
db.query(self.test_dir / Path("data/fasta_test_data"),
blast_format="",
headers=tuple(),
config={
"outfmt": "test",
"query": "test",
})
def test_query_wrong_type(self):
with self.assertRaises(TypeError):
db = blast.Database(source_dir=self.test_dir /
Path("data/fasta_test_data"),
name="test_db")
db.query("not a path obj",
blast_format="",
config={"task": "blastn-short"},
headers=tuple())
db.query(self.test_dir / Path("data/fasta_test_data"),
config="not a dict",
blast_format="",
headers=tuple())
def test_query_ok(self):
db = blast.Database(source_dir=self.test_dir /
Path("data/blast_query_data"),
name="test_db")
db.create()
expected = pd.DataFrame(columns=['Virus', 'Host', 'Score'],
data=[['seqs|1', 'seqs|1', 10],
['seqs|2', 'seqs|2', 9]])
res = db.query(self.test_dir / Path("data/blast_query_data"),
config={"task": "blastn-short"},
blast_format="10 qseqid sseqid score",
headers=('Virus', 'Host', 'Score'))
self.assertIsInstance(res, pd.DataFrame)
self.assertTrue(expected.equals(res))
def test_create_call(self, mock: Mock):
blast.Database(source_dir=self.test_dir / Path("data/fasta_test_data"),
name="test_db").create()
mock.assert_called_once()
def test_aggregate_wrong_type(self):
with self.assertRaises(TypeError):
db = blast.Database(source_dir=Path(""), name="test_db")
db._aggregate("not a path obj", Path("blast_input.fasta"))
db._aggregate(Path(""), "not a path obj")
def test_database_init_ok(self):
try:
blast.Database(source_dir=self.test_dir / Path("data"),
name="test_db")
except:
self.fail("Valid path caused exception.")
def test_database_init_wrong_instance(self):
with self.assertRaises(TypeError):
blast.Database(source_dir="not a path object", name="")
blast.Database(source_dir=Path(""), name="not a str")
def test_aggregate_empty(self):
with self.assertRaises(ValueError):
blast.Database(source_dir=Path(""), name="test_db")._aggregate(
self.test_dir / Path("data/fasta_test_empty_data"),
Path("blast_input.fasta"))
def test_aggregate_ok(self):
blast.Database(source_dir=Path(""), name="test_db")._aggregate(
self.test_dir / Path("data/fasta_test_data"),
Path("blast_input.fasta"))
self.assertTrue(Path("blast_input.fasta").exists())
self.assertTrue(os.path.getsize(Path("blast_input.fasta")) > 0)
def test_repair_wrong_type(self):
db = blast.Database(source_dir=self.test_dir /
Path("data/fasta_test_data"),
name="test_db")
with self.assertRaises(TypeError):
db.repair_fasta("not a path object")
def test_repair_wrong_file(self):
db = blast.Database(source_dir=Path(""), name="test_db")
with self.assertRaises(FileNotFoundError):
db.repair_fasta(self.test_dir / Path("data/fasta_test_data"))
