def test_sequences_to_file(self):
"""sequences_to_file should write a standard format FASTA file."""
self.seq_test_fp = get_tmp_filename_as_str(\
prefix='ExcludeByBlastTests_',suffix='.fasta')
self._paths_to_clean_up.append(self.seq_test_fp)
ids = ["bth:BT_0001","hsa:8355"]
seqs=seqs_from_file(ids, open(self.query_fp).readlines())
sequences_to_file(seqs, self.seq_test_fp)
self.assertEqual(open(self.seq_test_fp).readlines(),\
open(self.query_fp).readlines())
def test_seqs_from_file(self):
"""seqs_from_file should extract labels,seqs for specified ids"""
ids = "bth:BT_0001"
seqs = seqs_from_file(ids, open(self.query_fp).readlines())
all_results = []
for label, seq in seqs:
all_results.append((label, seq))
self.assertEqual(1, len(all_results)) # should return only 1 entry
# fn should return version lacking ">" and newlines
self.assertEqual(all_results[0],
(TEST_BLAST_DB_LINES[2].strip(">").strip(),
TEST_BLAST_DB_LINES[3].strip()))
def test_seqs_from_file(self):
"""seqs_from_file should extract labels,seqs for specified ids"""
ids = "bth:BT_0001"
seqs = seqs_from_file(ids, open(self.query_fp).readlines())
all_results = []
for label, seq in seqs:
all_results.append((label, seq))
self.assertEqual(1, len(all_results)) # should return only 1 entry
# fn should return version lacking ">" and newlines
self.assertEqual(all_results[0],
(TEST_BLAST_DB_LINES[2].strip(">").strip(),
TEST_BLAST_DB_LINES[3].strip()))
