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()))