class TestFastaParser(unittest.TestCase):
def setUp(self):
self.fasta_parser = FastaParser()
self.example_data = ExampleData()
def test_parse_1(self):
fasta_fh = StringIO(self.example_data.fasta_seqs_1)
self.assertEqual(
list(self.fasta_parser.entries(fasta_fh)),
[('test_1 a random sequence', 'TTTAGAAATTACACA'),
('test_2 another random sequence', 'ACGAGAAATTAAATTAAATT'),
('test_3 another random sequence', 'TAGAGACATTGGATTTTATT')])
def test_parse_empty_file(self):
fasta_fh = StringIO("")
self.assertEqual(
list(self.fasta_parser.entries(fasta_fh)), [])
def test_single_entry_file_header(self):
fasta_fh = StringIO(self.example_data.fasta_seqs_2)
self.assertEqual(self.fasta_parser.single_entry_file_header(fasta_fh),
"test_4 a random sequence")
def test_header_id_1(self):
self.assertEqual(
self.fasta_parser.header_id("seq_10101 An important protein"),
"seq_10101")
def test_header_id_2(self):
self.assertEqual(
self.fasta_parser.header_id("seq_10101\tAn important protein"),
"seq_10101")
def _ref_ids_to_file(self, ref_seq_paths):
"""Translate the reference ID to file paths."""
ref_ids_to_file = {}
fasta_parser = FastaParser()
for ref_seq_path in ref_seq_paths:
ref_seq_file = os.path.basename(ref_seq_path)
with open(ref_seq_path) as ref_seq_fh:
ref_seq_id = fasta_parser.header_id(
fasta_parser.single_entry_file_header(ref_seq_fh))
ref_ids_to_file[ref_seq_id] = ref_seq_file
return ref_ids_to_file
def _ref_ids_to_file(self, ref_seq_paths):
"""Translate the reference ID to file paths."""
ref_ids_to_file = {}
fasta_parser = FastaParser()
for ref_seq_path in ref_seq_paths:
ref_seq_file = os.path.basename(ref_seq_path)
with open(ref_seq_path) as ref_seq_fh:
ref_seq_id = fasta_parser.header_id(
fasta_parser.single_entry_file_header(ref_seq_fh))
ref_ids_to_file[ref_seq_id] = ref_seq_file
return ref_ids_to_file
class TestFastaParser(unittest.TestCase):
def setUp(self):
self.fasta_parser = FastaParser()
self.example_data = ExampleData()
def test_parse_1(self):
fasta_fh = StringIO(self.example_data.fasta_seqs_1)
self.assertEqual(
list(self.fasta_parser.entries(fasta_fh)),
[
("test_1 a random sequence", "TTTAGAAATTACACA"),
("test_2 another random sequence", "ACGAGAAATTAAATTAAATT"),
("test_3 another random sequence", "TAGAGACATTGGATTTTATT"),
],
)
def test_parse_empty_file(self):
fasta_fh = StringIO("")
self.assertEqual(list(self.fasta_parser.entries(fasta_fh)), [])
def test_single_entry_file_header(self):
fasta_fh = StringIO(self.example_data.fasta_seqs_2)
self.assertEqual(
self.fasta_parser.single_entry_file_header(fasta_fh),
"test_4 a random sequence",
)
def test_header_id_1(self):
self.assertEqual(
self.fasta_parser.header_id("seq_10101 An important protein"),
"seq_10101",
)
def test_header_id_2(self):
self.assertEqual(
self.fasta_parser.header_id("seq_10101\tAn important protein"),
"seq_10101",
)
