def test_order_is_retained(self):
# BPP(Breakpoint(1:1925143-1925155R), Breakpoint(1:1925144L), opposing=False)
# >> BPP(Breakpoint(1:1925144L), Breakpoint(1:1925144-1925158R), opposing=False)
# >> BPP(Breakpoint(1:1925143L), Breakpoint(1:1925143-1925158R), opposing=False)
pairs = [
BreakpointPair(
Breakpoint('2', 1925144, 1925144, 'L'),
Breakpoint('2', 1925144, 1925158, 'R'),
event_type='deletion',
opposing_strands=False,
),
BreakpointPair(
Breakpoint('2', 1925143, 1925143, 'L'),
Breakpoint('2', 1925143, 1925158, 'R'),
event_type='deletion',
opposing_strands=False,
),
]
mapping = merge_breakpoint_pairs(pairs, 100, 25)
for merge, inputs in mapping.items():
print(merge)
print(inputs)
self.assertEqual(1, len(mapping))
merge = list(mapping)[0]
self.assertEqual('L', merge.break1.orient)
self.assertEqual('R', merge.break2.orient)
def test_clustering_events(self):
# this file contains 2 events that should be clustered and produce a valid bpp
bpps = []
for bpp in sorted(
read_bpp_from_input_file(CLUSTERED_EVENTS), key=lambda x: (x.break1.chr, x.break2.chr)
):
if bpp.data[COLUMNS.protocol] == PROTOCOL.GENOME:
bpps.append(bpp)
print(bpp)
self.assertEqual(2, len(bpps))
clusters = merge_breakpoint_pairs(bpps, 200, 25)
self.assertEqual(1, len(clusters))
for cluster, input_pairs in sorted(
clusters.items(), key=lambda x: (x[1][0].break1.chr, x[1][0].break2.chr)
):
print(cluster)
for ip in input_pairs:
print('\t', ip)
print(cluster.flatten())
# BPP(Breakpoint(15:67333604L), Breakpoint(15:67333606R), opposing=False)
self.assertEqual('L', cluster.break1.orient)
self.assertEqual('R', cluster.break2.orient)
self.assertEqual('15', cluster.break1.chr)
self.assertEqual('15', cluster.break2.chr)
self.assertEqual(67333604, cluster.break1.start)
self.assertEqual(67333606, cluster.break2.start)
self.assertEqual(67333604, cluster.break1.end)
self.assertEqual(67333606, cluster.break2.end)
def test_events_separate(self):
bpps = [
BreakpointPair(
Breakpoint('4', 157002032, 157002046, orient='L'),
Breakpoint('4', 157002343, 157002343, orient='R'),
event_type=SVTYPE.DEL,
untemplated_seq='',
protocol='genome',
tracking_id='manta-MantaDEL:55718:0:0:1:0:0',
),
BreakpointPair(
Breakpoint('4', 156935061, orient='L'),
Breakpoint('4', 156935245, orient='R'),
event_type=SVTYPE.DEL,
untemplated_seq='',
protocol='genome',
tracking_id='delly-DEL00011007',
),
BreakpointPair(
Breakpoint('4', 157002046, orient='L'),
Breakpoint('4', 157002358, orient='R'),
event_type=SVTYPE.DEL,
untemplated_seq='',
protocol='genome',
tracking_id='delly-DEL00011008',
),
]
mapping = merge_breakpoint_pairs(bpps, 100, 25, verbose=True)
self.assertEqual(2, len(mapping))
def test_merging_identical_large_inputs(self):
b1 = BreakpointPair(Breakpoint(11, 12856838, 12897006, 'L'), Breakpoint(11, 12856838, 12897006, 'R'), opposing_strands=False)
b2 = BreakpointPair(Breakpoint(11, 12856838, 12897006, 'L'), Breakpoint(11, 12856838, 12897006, 'R'), opposing_strands=False)
mapping = merge_breakpoint_pairs([b1, b2], 100, 25, verbose=True)
self.assertEqual(1, len(mapping))
merge = list(mapping)[0]
self.assertEqual(2, len(mapping[merge]))
self.assertEqual('L', merge.break1.orient)
self.assertEqual('R', merge.break2.orient)
self.assertEqual('11', merge.break1.chr)
self.assertEqual('11', merge.break2.chr)
self.assertEqual(12856838, merge.break1.start)
self.assertEqual(12856838, merge.break2.start)
self.assertEqual(12897006, merge.break1.end)
self.assertEqual(12897006, merge.break2.end)
def test_mocked_events(self):
# none of the 24 events in the mocked file should cluster together
# if we change the mock file we may need to update this function
bpps = []
for bpp in sorted(read_bpp_from_input_file(FULL_BASE_EVENTS), key=lambda x: (x.break1.chr, x.break2.chr)):
if bpp.data[COLUMNS.protocol] == PROTOCOL.GENOME:
bpps.append(bpp)
print(bpp)
self.assertEqual(28, len(bpps))
clusters = merge_breakpoint_pairs(bpps, 10, 10)
for cluster, input_pairs in sorted(clusters.items(), key=lambda x: (x[1][0].break1.chr, x[1][0].break2.chr)):
print(cluster)
for ip in input_pairs:
print('\t', ip)
self.assertEqual(1, len(input_pairs))
self.assertEqual(len(bpps), len(clusters))