def test_non_specific_error(self):
b1 = Breakpoint(REF_CHR,
740,
745,
strand=STRAND.POS,
orient=ORIENT.RIGHT)
b2 = Breakpoint(REF_CHR, 747, strand=STRAND.POS, orient=ORIENT.LEFT)
bpp = BreakpointPair(b1, b2)
with pytest.raises(AttributeError):
bpp.breakpoint_sequence_homology(REFERENCE_GENOME)
def test_left_pos_right_pos(self):
b1 = Breakpoint(REF_CHR, 157, strand=STRAND.POS, orient=ORIENT.LEFT)
b2 = Breakpoint(REF_CHR, 1788, strand=STRAND.POS, orient=ORIENT.RIGHT)
bpp = BreakpointPair(b1, b2)
assert bpp.breakpoint_sequence_homology(REFERENCE_GENOME) == ('CAATGC',
'')
b1 = Breakpoint(REF_CHR, 589, strand=STRAND.POS, orient=ORIENT.LEFT)
b2 = Breakpoint(REF_CHR, 704, strand=STRAND.POS, orient=ORIENT.RIGHT)
bpp = BreakpointPair(b1, b2)
assert bpp.breakpoint_sequence_homology(REFERENCE_GENOME) == ('TTAA',
'ATAGC')
def test_close_del(self):
# ....TT|TT....
b1 = Breakpoint(REF_CHR, 1001, strand=STRAND.POS, orient=ORIENT.LEFT)
b2 = Breakpoint(REF_CHR, 1002, strand=STRAND.POS, orient=ORIENT.RIGHT)
bpp = BreakpointPair(b1, b2)
self.assertEqual(('', ''),
bpp.breakpoint_sequence_homology(REFERENCE_GENOME))
def test_right_neg_right_pos(self):
# CCC|AAA ------------ TTT|GGG
# GGG GGG
# AAA AAA
b1 = Breakpoint(REF_CHR, 1460, strand=STRAND.NEG, orient=ORIENT.RIGHT)
b2 = Breakpoint(REF_CHR, 2915, strand=STRAND.POS, orient=ORIENT.RIGHT)
bpp = BreakpointPair(b1, b2)
assert bpp.breakpoint_sequence_homology(REFERENCE_GENOME) == ('AAA',
'GGG')
def test_left_neg_left_pos(self):
# CCC|AAA ------------ TTT|GGG
# CCC CCC
# TTT TTT
b1 = Breakpoint(REF_CHR, 1459, strand=STRAND.NEG, orient=ORIENT.LEFT)
b2 = Breakpoint(REF_CHR, 2914, strand=STRAND.POS, orient=ORIENT.LEFT)
bpp = BreakpointPair(b1, b2)
assert bpp.breakpoint_sequence_homology(REFERENCE_GENOME) == ('CCC',
'TTT')
def test_close_dup(self):
# ....GATACATTTCTTCTTGAAAA...
# -------------<=============
# ===============>-----------
# -------------CT-CT--------- first break homology
# ------------T--T----------- second break homology
b1 = Breakpoint(REF_CHR, 745, strand=STRAND.POS, orient=ORIENT.RIGHT)
b2 = Breakpoint(REF_CHR, 747, strand=STRAND.POS, orient=ORIENT.LEFT)
bpp = BreakpointPair(b1, b2)
assert bpp.breakpoint_sequence_homology(REFERENCE_GENOME) == ('CT',
'TT')
