def test_insertion_to_duplication(self):
# BPP(Breakpoint(3:60204611L), Breakpoint(3:60204612R), opposing=False, seq='CATACATACATACATACATACATACATACATA')
# insertion contig [seq2] contig_alignment_score: 0.99, contig_alignment_mq: Interval(255, 255)
# (3:60132614[seq2]140=71788D69=32I86=, None))
bpp = BreakpointPair(
Breakpoint('3', 60204611, orient='L'),
Breakpoint('3', 60204612, orient='R'),
untemplated_seq='CATACATACATACATACATACATACATACATA',
opposing_strands=False)
reference_genome = {
'3':
MockObject(seq=MockLongString(
'CAGGGTCTGAGCTCTTAACTCTATACTGCCTACATACATACATACATACATACATATATACATACATATATAAATT',
offset=60204555))
}
print(reference_genome['3'].seq[60204588:60204588 + 8], 'CATACATA')
setattr(bpp, 'read1', MockObject(query_sequence='', query_name=None))
setattr(bpp, 'read2', None)
event = align.convert_to_duplication(bpp, reference_genome)
print(event)
self.assertEqual(ORIENT.RIGHT, event.break1.orient)
self.assertEqual(60204588, event.break1.start)
self.assertEqual(ORIENT.LEFT, event.break2.orient)
self.assertEqual(60204611, event.break2.start)
# CATACATACATACATACATACATACATACATA
# ........................********
self.assertEqual('CATACATA', event.untemplated_seq)
def test_single_duplication_with_trailing_untemp(self):
r = MockRead(query_sequence=(
'GGATGATTTACCTTGGGTAATGAAACTCA'
'GATTTTGCTGTTGTTTTTGTTC'
'GATTTTGCTGTTGTTTTTGTTC'
'GTCAA'
'CAAAGTGTTTTATACTGATAAAGCAACCCCGGTTTAGCATTGCCATTGGTAA'),
query_name='duplication_with_untemp',
reference_id=2,
reference_name='reference3',
reference_start=1497,
cigar=[(CIGAR.EQ, 51), (CIGAR.I, 27), (CIGAR.EQ, 52)],
is_reverse=False)
# repeat: GATTTTGCTGTTGTTTTTGTTC
print(r)
print(REFERENCE_GENOME['reference3'][1497:1497 + 51])
print(REFERENCE_GENOME['reference3'][1548 - 21:1548 + 1])
bpp = align.call_read_events(r)[0]
print(bpp)
bpp = align.convert_to_duplication(bpp, REFERENCE_GENOME)
print(bpp)
self.assertEqual('GTCAA', bpp.untemplated_seq)
self.assertEqual(ORIENT.RIGHT, bpp.break1.orient)
self.assertEqual(ORIENT.LEFT, bpp.break2.orient)
self.assertEqual(bpp.break2.start, 1548)
self.assertEqual(bpp.break1.start, 1527)
def test_single_duplication_with_no_untemp(self):
r = MockRead(query_sequence=(
'GGATGATTTACCTTGGGTAATGAAACTCAGATTTTGCTGTTGTTTTTGTTCGATTTTGCTGTTGTTTTTGTTCCAAAGTGTTTTATACTGATAAAGCAACC'
'CCGGTTTAGCATTGCCATTGGTAA'),
query_name='duplication_with_untemp',
reference_id=2,
reference_name='reference3',
reference_start=1497,
cigar=[(CIGAR.EQ, 51), (CIGAR.I, 22), (CIGAR.EQ, 52)],
is_reverse=False)
# repeat: GATTTTGCTGTTGTTTTTGTTC
bpp = align.convert_to_duplication(
align.call_read_events(r)[0], REFERENCE_GENOME)
self.assertEqual('', bpp.untemplated_seq)
self.assertEqual(ORIENT.RIGHT, bpp.break1.orient)
self.assertEqual(ORIENT.LEFT, bpp.break2.orient)
self.assertEqual(bpp.break2.start, 1548)
self.assertEqual(bpp.break1.start, 1527)
def test_single_bp_insertion(self):
bpp = BreakpointPair(
Breakpoint('3', 121, orient='L'), Breakpoint('3', 122, orient='R'),
untemplated_seq='T',
opposing_strands=False
)
reference_genome = {'3': MockObject(
seq=MockLongString('ATCGAGCTACGGATCTTTTTTCGATCGATCAATA', offset=100))}
print(reference_genome['3'].seq[120 - 10:121])
setattr(bpp, 'read1', MockObject(query_sequence='', query_name=None))
setattr(bpp, 'read2', None)
event = align.convert_to_duplication(bpp, reference_genome)
print(event)
self.assertEqual(ORIENT.RIGHT, event.break1.orient)
self.assertEqual(121, event.break1.start)
self.assertEqual(ORIENT.LEFT, event.break2.orient)
self.assertEqual(121, event.break2.start)
self.assertEqual('', event.untemplated_seq)