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)