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 test_fasta_parser():
# Define some dummy data & parser object
fasta_parser = FastaParser()
fasta_seqs_1 = """>test_1 a random sequence
TTTAG
AAATT
ACACA
>test_2 another random sequence
ACGAG
AAATT
AAATT
AAATT
>test_3 another random sequence
TAGAG
ACATT
GGATT
TTATT
"""
fasta_seqs_2 = """>test_4 a random sequence
TTTAG
AAATT
ACACA
"""
# test fasta entry
fasta_fh = StringIO(fasta_seqs_1)
assert list(fasta_parser.entries(fasta_fh)) == [
('test_1 a random sequence', 'TTTAGAAATTACACA'),
('test_2 another random sequence', 'ACGAGAAATTAAATTAAATT'),
('test_3 another random sequence', 'TAGAGACATTGGATTTTATT')
]
# test empty fasta file
fasta_empty_fh = StringIO("")
assert list(fasta_parser.entries(fasta_empty_fh)) == []
# test single entry file header
fasta_header_fh = StringIO(fasta_seqs_2)
assert fasta_parser.single_entry_file_header(
fasta_header_fh) == "test_4 a random sequence"
# test header id 1
assert fasta_parser.header_id(
"seq_10101 An important protein") == "seq_10101"
# test header id 2
assert fasta_parser.header_id(
"seq_10101\tAn important protein") == "seq_10101"
def setUp(self):
self.fasta_parser = FastaParser()
self.example_data = ExampleData()
def __init__(self):
self.fasta_parser = FastaParser()
