def test_scanner_init_ok(self):
try:
trna.tRNAScanner(self.test_dir / Path("data/test_trnascan_host"),
self.test_dir / Path("data/test_trnascan_phage"),
"trna_db")
except:
self.fail("Valid path caused exception.")
def test_scanner_init_wrong_path(self):
with self.assertRaises(FileNotFoundError):
trna.tRNAScanner(self.test_dir / Path("data/not_existing"),
self.test_dir / Path("not_existing"),
"trna_db")
trna.tRNAScanner(self.test_dir / Path("data/blast_query_data/seqs.fasta"),
self.test_dir / Path("data/blast_query_data/seqs.fasta"),
"trna_db")
def test_scanner_creates(self):
t = trna.tRNAScanner(self.test_dir / Path("data/test_trnascan_host"),
self.test_dir / Path("data/test_trnascan_phage"),
"trna_db")
host = t.scan(t.source_dir, output_filename="test_host_trnas.fasta")
t.create(host)
self.assertTrue(all(map(lambda x: Path(x).exists(), ['trna_db.nhr', 'trna_db.nin', 'trna_db.nsq'])))
t.clear_files()
def test_scanner_query(self):
t = trna.tRNAScanner(self.test_dir / Path("data/test_trnascan_host"),
self.test_dir / Path("data/test_trnascan_phage"),
"trna_db")
host = t.scan(t.source_dir, output_filename="test_host_trnas.fasta")
phage = t.scan(t.target_dir, output_filename="test_phage_trnas.fasta")
t.create(host)
res = t.query(phage, {"task": "blastn"}, blast_format="10 qseqid sseqid score",
headers=("Virus", "Host", "Score"))
self.assertTrue(len(res) == 23)
t.clear_files()
def test_scanner_scans(self):
t = trna.tRNAScanner(self.test_dir / Path("data/test_trnascan_host"),
self.test_dir / Path("data/test_trnascan_phage"),
"trna_db")
host = t.scan(t.source_dir, output_filename="test_host_trnas.fasta")
phage = t.scan(t.target_dir, output_filename="test_phage_trnas.fasta")
self.assertTrue(host.exists())
self.assertTrue(phage.exists())
self.assertTrue(len(list(seq for seq in SeqIO.parse(host, 'fasta'))) > 0)
host.unlink()
phage.unlink()
def test_scanner_init_wrong_instance(self):
with self.assertRaises(TypeError):
trna.tRNAScanner("not path",
self.test_dir / Path("data/test_trnascan_phage"),
"trna_db")
trna.tRNAScanner(self.test_dir / Path("data/test_trnascan_host"),
"not path",
"trna_db")
trna.tRNAScanner(self.test_dir / Path("data/test_trnascan_host"),
self.test_dir / Path("data/test_trnascan_phage"),
Path("not a str"))