def test_ref_deletion(self): v3loop_ref = 'TGTACAAGACCCAACAAC' counts = [(("TGTACA---AGACCCAAC", "TGTACAGGGAGACCCAAC"), 2)] hiv_seed = "ATGTACAGGGAGACCCAACAAC" aligned_csv = DummyFile() expected_aligned_csv = """\ refname,qcut,rank,count,offset,seq HIV1-CON-XX-Consensus-seed,15,0,2,1,TGTACA---AGACCCAAC """ list(write_aligned_reads(counts, aligned_csv, hiv_seed, v3loop_ref)) self.assertEqual(expected_aligned_csv, aligned_csv.getvalue())
def test_ref_deletion(self): v3loop_ref = 'TGTACAAGACCCAACAAC' counts = [(("TGTACA---AGACCCAAC", "TGTACAGGGAGACCCAAC"), 2)] hiv_seed = "ATGTACAGGGAGACCCAACAAC" aligned_csv = DummyFile() expected_aligned_csv = """\ refname,qcut,rank,count,offset,seq HIV1-CON-XX-Consensus-seed,15,0,2,1,TGTACA---AGACCCAAC """ list(write_aligned_reads(counts, aligned_csv, hiv_seed, v3loop_ref)) self.assertEqual(expected_aligned_csv, aligned_csv.getvalue())
def test_ref_insertion(self): v3loop_ref = 'TGTACAAGACCCAACAAC' counts = [(("TGTACAAGACCCAAC", "TGTACAAGACCCAAC"), 2)] # inserted codon ^^^ shouldn't be included in aligned seq. hiv_seed = "ATGTACACCCAACAAC" aligned_csv = DummyFile() expected_aligned_csv = """\ refname,qcut,rank,count,offset,seq HIV1-CON-XX-Consensus-seed,15,0,2,1,TGTACACCCAAC """ list(write_aligned_reads(counts, aligned_csv, hiv_seed, v3loop_ref)) self.assertEqual(expected_aligned_csv, aligned_csv.getvalue())
def test_ref_insertion(self): v3loop_ref = 'TGTACAAGACCCAACAAC' counts = [(("TGTACAAGACCCAAC", "TGTACAAGACCCAAC"), 2)] # inserted codon ^^^ shouldn't be included in aligned seq. hiv_seed = "ATGTACACCCAACAAC" aligned_csv = DummyFile() expected_aligned_csv = """\ refname,qcut,rank,count,offset,seq HIV1-CON-XX-Consensus-seed,15,0,2,1,TGTACACCCAAC """ list(write_aligned_reads(counts, aligned_csv, hiv_seed, v3loop_ref)) self.assertEqual(expected_aligned_csv, aligned_csv.getvalue())
def test_counts(self): v3loop_ref = 'TGTACAAGACCCAACAAC' counts = [(("TGTACAAGACCCAAC", "TGTACAAGACCCAAC"), 2), (("TGTACAAGACCCAAC", "AGAACAAGACCCAAC"), 1)] seed = "AAAAATGTACAAGACACAACAAC" aligned_csv = DummyFile() expected_aligned_csv = """\ refname,qcut,rank,count,offset,seq HIV1-CON-XX-Consensus-seed,15,0,2,5,TGTACAAGACCCAAC HIV1-CON-XX-Consensus-seed,15,1,1,5,AGAACAAGACCCAAC """ counts2 = list(write_aligned_reads(counts, aligned_csv, seed, v3loop_ref)) self.assertEqual(expected_aligned_csv, aligned_csv.getvalue()) self.assertEqual(counts, counts2)