def test_read_skip_sequence(self):
fasta = os.path.join(self.formats_folder, "fasta")
with easel.SequenceFile(fasta) as f:
seq = f.read()
self.assertEqual(seq.name, b"SNRPA_DROME")
self.assertNotEqual(seq.sequence, "")
with easel.SequenceFile(fasta) as f:
seq = f.read(skip_sequence=True)
self.assertEqual(seq.name, b"SNRPA_DROME")
self.assertEqual(seq.sequence, "")
def test_readformat_genbank(self):
gbk = os.path.join(self.formats_folder, "genbank")
# check reading an EMBL file works
with easel.SequenceFile(gbk, "genbank") as f:
seq = f.read()
self.assertNotEqual(seq.accession, b"")
# check reading an GenBank file without specifying the format works too
with easel.SequenceFile(gbk) as f:
seq2 = f.read()
self.assertNotEqual(seq2.accession, b"")
# check reading an GenBank file while giving another format fails
with easel.SequenceFile(gbk, "fasta") as f:
self.assertRaises(ValueError, f.read)
def test_readformat_fasta(self):
for filename in ["fasta", "fasta.2", "fasta.odd.1"]:
fasta = os.path.join(self.formats_folder, filename)
# check reading a FASTA file works
with easel.SequenceFile(fasta, "fasta") as f:
seq = f.read()
self.assertNotEqual(seq.name, b"")
# check reading a FASTA file without specifying the format works too
with easel.SequenceFile(fasta) as f:
seq2 = f.read()
self.assertNotEqual(seq2.name, b"")
# check reading a FASTA file while giving another format fails
with easel.SequenceFile(fasta, "embl") as f:
self.assertRaises(ValueError, f.read)
def test_iter(self):
fasta = os.path.join(self.formats_folder, "fasta")
with easel.SequenceFile(fasta) as f:
seq1, seq2 = list(f)
self.assertEqual(seq1.name, b"SNRPA_DROME")
self.assertEqual(seq2.name, b"SNRPA_HUMAN")
def test_init_error_unknownformat(self):
with self.assertRaises(ValueError):
_file = easel.SequenceFile("file.x", format="nonsense")
def test_guess_alphabet(self):
embl = os.path.join(self.formats_folder, "embl")
with easel.SequenceFile(embl, "embl") as f:
self.assertEqual(f.guess_alphabet(), easel.Alphabet.dna())
def test_readformat_fasta_error(self):
fasta = os.path.join(self.formats_folder, "fasta.bad.1")
with easel.SequenceFile(fasta, "fasta") as f:
self.assertRaises(ValueError, f.read)