def test_duplication(self):
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.POS, orient=ORIENT.RIGHT),
Breakpoint(1, 10, 11, strand=STRAND.POS, orient=ORIENT.LEFT))
self.assertEqual({SVTYPE.DUP}, BreakpointPair.classify(b))
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.POS, orient=ORIENT.RIGHT),
Breakpoint(1, 10, 11, strand=STRAND.POS, orient=ORIENT.LEFT))
self.assertEqual({SVTYPE.DUP}, BreakpointPair.classify(b))
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NEG, orient=ORIENT.RIGHT),
Breakpoint(1, 10, 11, strand=STRAND.NEG, orient=ORIENT.LEFT))
self.assertEqual({SVTYPE.DUP}, BreakpointPair.classify(b))
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.POS, orient=ORIENT.RIGHT),
Breakpoint(1, 10, 11, strand=STRAND.POS, orient=ORIENT.NS))
self.assertEqual({SVTYPE.DUP}, BreakpointPair.classify(b))
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NEG, orient=ORIENT.RIGHT),
Breakpoint(1, 10, 11, strand=STRAND.NEG, orient=ORIENT.NS))
self.assertEqual({SVTYPE.DUP}, BreakpointPair.classify(b))
def test_translocation(self):
b = BreakpointPair(
Breakpoint(1, 1, 2, ORIENT.RIGHT),
Breakpoint(2, 1, 2, ORIENT.LEFT),
opposing_strands=False,
)
BreakpointPair.classify(b)
def test_inverted_translocation(self):
b = BreakpointPair(
Breakpoint(1, 1, 2, ORIENT.LEFT),
Breakpoint(2, 1, 2, ORIENT.LEFT),
opposing_strands=True,
)
BreakpointPair.classify(b)
def test_deletion_with_useq(self):
bpp = BreakpointPair(Breakpoint('1', 6964, orient='L'),
Breakpoint('1', 7040, orient='R'),
opposing=False,
untemplated_seq='CCCT')
self.assertEqual(sorted([SVTYPE.DEL, SVTYPE.INS]),
sorted(BreakpointPair.classify(bpp)))
def distance(x, y):
return Interval(abs(x - y))
net_size = BreakpointPair.net_size(bpp, distance)
self.assertEqual(Interval(-71), net_size)
self.assertEqual(sorted([SVTYPE.DEL]),
sorted(BreakpointPair.classify(bpp, distance)))
def test_insertion(self):
b = BreakpointPair(
Breakpoint(1, 1, 1, strand=STRAND.NS, orient=ORIENT.LEFT),
Breakpoint(1, 2, 2, strand=STRAND.NS, orient=ORIENT.RIGHT),
opposing_strands=False,
)
self.assertEqual(sorted([SVTYPE.INS]), sorted(BreakpointPair.classify(b)))
def test_deletion(self):
b = BreakpointPair(
Breakpoint(1, 1, 1, strand=STRAND.NS, orient=ORIENT.LEFT),
Breakpoint(1, 3, 3, strand=STRAND.NS, orient=ORIENT.RIGHT),
opposing_strands=False,
untemplated_seq='',
)
self.assertEqual(sorted([SVTYPE.DEL]), sorted(BreakpointPair.classify(b)))
def test_no_type(self):
b = BreakpointPair(
Breakpoint(1, 1, 1, strand=STRAND.NS, orient=ORIENT.LEFT),
Breakpoint(1, 2, 2, strand=STRAND.NS, orient=ORIENT.RIGHT),
opposing_strands=False,
untemplated_seq='',
)
self.assertEqual(set(), BreakpointPair.classify(b))
def test_deletion_or_insertion(self):
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.POS, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.POS, orient=ORIENT.RIGHT),
)
assert sorted(BreakpointPair.classify(b)) == sorted([SVTYPE.DEL, SVTYPE.INS])
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.POS, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.NS, orient=ORIENT.RIGHT),
opposing_strands=False,
)
assert sorted(BreakpointPair.classify(b)) == sorted([SVTYPE.DEL, SVTYPE.INS])
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NEG, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.NEG, orient=ORIENT.RIGHT),
)
assert sorted(BreakpointPair.classify(b)) == sorted([SVTYPE.DEL, SVTYPE.INS])
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NEG, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.NS, orient=ORIENT.RIGHT),
opposing_strands=False,
)
assert sorted(BreakpointPair.classify(b)) == sorted([SVTYPE.DEL, SVTYPE.INS])
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NS, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.POS, orient=ORIENT.RIGHT),
opposing_strands=False,
)
assert sorted(BreakpointPair.classify(b)) == sorted([SVTYPE.DEL, SVTYPE.INS])
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NS, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.NEG, orient=ORIENT.RIGHT),
opposing_strands=False,
)
assert sorted(BreakpointPair.classify(b)) == sorted([SVTYPE.DEL, SVTYPE.INS])
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NS, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.NS, orient=ORIENT.RIGHT),
opposing_strands=False,
)
assert sorted(BreakpointPair.classify(b)) == sorted([SVTYPE.DEL, SVTYPE.INS])
def test_inversion(self):
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.POS, orient=ORIENT.RIGHT),
Breakpoint(1, 10, 11, strand=STRAND.NEG, orient=ORIENT.RIGHT),
)
assert BreakpointPair.classify(b) == {SVTYPE.INV}
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NEG, orient=ORIENT.RIGHT),
Breakpoint(1, 10, 11, strand=STRAND.POS, orient=ORIENT.RIGHT),
)
assert BreakpointPair.classify(b) == {SVTYPE.INV}
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.POS, orient=ORIENT.RIGHT),
Breakpoint(1, 10, 11, strand=STRAND.NEG, orient=ORIENT.NS),
)
assert BreakpointPair.classify(b) == {SVTYPE.INV}
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NEG, orient=ORIENT.RIGHT),
Breakpoint(1, 10, 11, strand=STRAND.POS, orient=ORIENT.NS),
)
assert BreakpointPair.classify(b) == {SVTYPE.INV}
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.POS, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.NEG, orient=ORIENT.LEFT),
)
assert BreakpointPair.classify(b) == {SVTYPE.INV}
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NEG, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.POS, orient=ORIENT.LEFT),
)
assert BreakpointPair.classify(b) == {SVTYPE.INV}
def test_deletion_no_distance_error(self):
bpp = BreakpointPair(Breakpoint('1', 7039, orient='L'),
Breakpoint('1', 7040, orient='R'),
opposing=False)
self.assertEqual(sorted([SVTYPE.INS]),
sorted(BreakpointPair.classify(bpp)))
