def test_nonspecific_refseq(self):
# null matches anything
assert match.compare_positional_variants(
{'break1Start': {'pos': 1}, 'refSeq': 'T'}, {'break1Start': {'pos': 1}}
)
assert match.compare_positional_variants(
{'break1Start': {'pos': 1}}, {'break1Start': {'pos': 1}, 'refSeq': 'T'}
)
def test_refseq_length_mismatch(self):
assert not match.compare_positional_variants(
{'break1Start': {'pos': 1}, 'refSeq': '??'},
{'break1Start': {'pos': 1}, 'refSeq': 'T'},
)
assert not match.compare_positional_variants(
{'break1Start': {'pos': 1}, 'refSeq': '?'},
{'break1Start': {'pos': 1}, 'refSeq': 'TT'},
)
def test_nonspecific_altseq(self):
assert match.compare_positional_variants(
{'break1Start': {'pos': 1}}, {'break1Start': {'pos': 1}}
)
# null matches anything
assert match.compare_positional_variants(
{'break1Start': {'pos': 1}, 'untemplatedSeq': 'T'}, {'break1Start': {'pos': 1}}
)
assert match.compare_positional_variants(
{'break1Start': {'pos': 1}}, {'break1Start': {'pos': 1}, 'untemplatedSeq': 'T'}
)
def test_range_vs_sub(self):
sub = {
'break1Repr': 'p.G776',
'break1Start': {'@Class': 'ProteinPosition', 'pos': 776, 'refAA': 'G'},
'break2Repr': 'p.V777',
'break2Start': {'@Class': 'ProteinPosition', 'pos': 777, 'refAA': 'V'},
'reference1': 'ERBB2',
'type': 'insertion',
'untemplatedSeq': 'YVMA',
'untemplatedSeqSize': 4,
}
range_variant = {
'break1Repr': 'p.G776',
'break1Start': {'@Class': 'ProteinPosition', 'pos': 776, 'refAA': 'G'},
'break2Repr': 'p.?776',
'break2Start': None,
'refSeq': 'G',
'untemplatedSeq': 'VV',
}
assert not match.compare_positional_variants(sub, range_variant)
assert not match.compare_positional_variants(range_variant, sub)
def test_same_refseq_matches(self):
assert match.compare_positional_variants(
{'break1Start': {'pos': 1}, 'refSeq': 'R'},
{'break1Start': {'pos': 1}, 'refSeq': 'R'},
)
def test_diff_refseq(self):
assert not match.compare_positional_variants(
{'break1Start': {'pos': 1}, 'refSeq': 'M'},
{'break1Start': {'pos': 1}, 'refSeq': 'R'},
)
def test_same_altseq_matches(self):
assert match.compare_positional_variants(
{'break1Start': {'pos': 1}, 'untemplatedSeq': 'R'},
{'break1Start': {'pos': 1}, 'untemplatedSeq': 'R'},
)
def test_diff_altseq(self):
assert not match.compare_positional_variants(
{'break1Start': {'pos': 1}, 'untemplatedSeq': 'M'},
{'break1Start': {'pos': 1}, 'untemplatedSeq': 'R'},
)
def test_ambiguous_refseq(self, seq1, seq2):
# ambiguous AA matches anything the same length
assert match.compare_positional_variants(
{'break1Start': {'pos': 1}, 'refSeq': seq1},
{'break1Start': {'pos': 1}, 'refSeq': seq2},
)