class TestBasicAnalysis(unittest.TestCase):
def setUp(self):
aln_string = """
>seq1
GTCAGTCAGTCAGTCACCCC
>seq2
GTCAGTCAGTCAGTCACCCC
>seq3
ATCAATCAGTCAATCACCCC
"""
self.seqs = helpers.parse_fasta(aln_string)
self.aln = Alignment(self.seqs.values())
def test_consensus_reference(self):
self.assertEqual(str(self.aln.reference_sequence),
'GTCAGTCAGTCAGTCACCCC')
def test_hm_pos(self):
for result in self.aln.analyze(
(old_focus_pattern, old_control_pattern)):
hm_pos = result['hm_pos']
if result['sequence'] in ['seq1', 'seq2']:
self.assertFalse(hm_pos)
else:
self.assertTrue(hm_pos)
def test_hm_pos_indices(self):
hm_pos_indices = [1, 5, 13]
for result in self.aln.analyze(
(old_focus_pattern, old_control_pattern)):
if result['hm_pos']:
self.assertEqual(result['mut_columns'], hm_pos_indices)
else:
self.assertEqual(result['mut_columns'], [])
class TestBasicAnalysis(unittest.TestCase):
def setUp(self):
aln_string = """
>seq1
GTCAGTCAGTCAGTCACCCC
>seq2
GTCAGTCAGTCAGTCACCCC
>seq3
ATCAATCAGTCAATCACCCC
"""
self.seqs = helpers.parse_fasta(aln_string)
self.aln = Alignment(self.seqs.values())
def test_consensus_reference(self):
self.assertEqual(str(self.aln.reference_sequence), 'GTCAGTCAGTCAGTCACCCC')
def test_hm_pos(self):
for result in self.aln.analyze((old_focus_pattern, old_control_pattern)):
hm_pos = result['hm_pos']
if result['sequence'] in ['seq1', 'seq2']:
self.assertFalse(hm_pos)
else:
self.assertTrue(hm_pos)
def test_hm_pos_indices(self):
hm_pos_indices = [1, 5, 13]
for result in self.aln.analyze((old_focus_pattern, old_control_pattern)):
if result['hm_pos']:
self.assertEqual(result['mut_columns'], hm_pos_indices)
else:
self.assertEqual(result['mut_columns'], [])
class TestMutCounts(unittest.TestCase):
def setUp(self):
aln_string = """
>seq1
GGTGACGCT
>seq2
AGTAACGCT
>seq3
GGTAACACT
"""
ref_seq = Seq.Seq('GGTGACGCT')
self.aln = Alignment(helpers.parse_fasta(aln_string).values(), reference_sequence=ref_seq)
def __test_counts__(self, pattern, real_counts):
for result in self.aln.analyze(pattern):
seq_counts = [result[x] for x in ('focus_pos', 'control_pos', 'focus_neg', 'control_neg')]
seq_real_counts = real_counts[result['sequence']]
self.assertEqual(seq_counts, seq_real_counts)
def test_ga_counts(self):
self.__test_counts__(mut_pattern.GA, dict(
seq1=[0, 0, 1, 3],
seq2=[1, 1, 0, 2],
seq3=[1, 1, 0, 2]))
def test_gg_counts(self):
self.__test_counts__(mut_pattern.GG, dict(
seq1=[0, 0, 1, 3],
seq2=[1, 1, 0, 2],
seq3=[0, 2, 1, 1]))
def test_gr_counts(self):
self.__test_counts__(mut_pattern.GR, dict(
seq1=[0, 0, 2, 2],
seq2=[2, 0, 0, 2],
seq3=[1, 1, 1, 1]))
def test_gm_counts(self):
self.__test_counts__(mut_pattern.GM, dict(
seq1=[0, 0, 2, 2],
seq2=[1, 1, 1, 1],
seq3=[2, 0, 0, 2]))
def test_gv_counts(self):
self.__test_counts__(mut_pattern.GV, dict(
seq1=[0, 0, 3, 1],
seq2=[2, 0, 1, 1],
seq3=[2, 0, 1, 1]))
class TestMutCounts(unittest.TestCase):
def setUp(self):
aln_string = """
>seq1
GGTGACGCT
>seq2
AGTAACGCT
>seq3
GGTAACACT
"""
ref_seq = Seq.Seq('GGTGACGCT')
self.aln = Alignment(helpers.parse_fasta(aln_string).values(),
reference_sequence=ref_seq)
def __test_counts__(self, pattern, real_counts):
for result in self.aln.analyze(pattern):
seq_counts = [
result[x] for x in ('focus_pos', 'control_pos', 'focus_neg',
'control_neg')
]
seq_real_counts = real_counts[result['sequence']]
self.assertEqual(seq_counts, seq_real_counts)
def test_ga_counts(self):
self.__test_counts__(
mut_pattern.GA,
dict(seq1=[0, 0, 1, 3], seq2=[1, 1, 0, 2], seq3=[1, 1, 0, 2]))
def test_gg_counts(self):
self.__test_counts__(
mut_pattern.GG,
dict(seq1=[0, 0, 1, 3], seq2=[1, 1, 0, 2], seq3=[0, 2, 1, 1]))
def test_gr_counts(self):
self.__test_counts__(
mut_pattern.GR,
dict(seq1=[0, 0, 2, 2], seq2=[2, 0, 0, 2], seq3=[1, 1, 1, 1]))
def test_gm_counts(self):
self.__test_counts__(
mut_pattern.GM,
dict(seq1=[0, 0, 2, 2], seq2=[1, 1, 1, 1], seq3=[2, 0, 0, 2]))
def test_gv_counts(self):
self.__test_counts__(
mut_pattern.GV,
dict(seq1=[0, 0, 3, 1], seq2=[2, 0, 1, 1], seq3=[2, 0, 1, 1]))
class TestContextBasedEvaluation(unittest.TestCase):
def setUp(self):
ref_seq = helpers.parse_fasta("""
>all
GGGGGGGGGTGTGTGTGT""")
self.aln = Alignment(helpers.parse_fasta("""
>seq1
GGGGGGGGGTGTGTGTGT
>seq2
AGAGAGAGGTGTGTGTGT
>seq3
GGGGGGGGGTATATATAT
""").values(), reference_sequence = ref_seq['all'])
def test_gg(self):
for result in self.aln.analyze(mut_pattern.GG):
hm_pos = result['hm_pos']
if result['sequence'] == 'seq2':
self.assertTrue(hm_pos)
else:
self.assertFalse(hm_pos)
class TestContextBasedEvaluation(unittest.TestCase):
def setUp(self):
ref_seq = helpers.parse_fasta("""
>all
GGGGGGGGGTGTGTGTGT""")
self.aln = Alignment(helpers.parse_fasta("""
>seq1
GGGGGGGGGTGTGTGTGT
>seq2
AGAGAGAGGTGTGTGTGT
>seq3
GGGGGGGGGTATATATAT
""").values(),
reference_sequence=ref_seq['all'])
def test_gg(self):
for result in self.aln.analyze(mut_pattern.GG):
hm_pos = result['hm_pos']
if result['sequence'] == 'seq2':
self.assertTrue(hm_pos)
else:
self.assertFalse(hm_pos)
