def test_break2_strand_ns(self, tmp_path):
input_file = tmp_path / "inputs.tsv"
input_file.write_text(
mock_file_content({
COLUMNS.break1_chromosome: '1',
COLUMNS.break1_position_start: 1,
COLUMNS.break1_position_end: 1,
COLUMNS.break1_strand: STRAND.POS,
COLUMNS.break1_orientation: ORIENT.LEFT,
COLUMNS.break2_chromosome: '1',
COLUMNS.break2_position_start: 10,
COLUMNS.break2_position_end: 10,
COLUMNS.break2_strand: STRAND.NS,
COLUMNS.break2_orientation: ORIENT.RIGHT,
COLUMNS.stranded: True,
COLUMNS.opposing_strands: False,
}))
with pytest.raises(NotSpecifiedError) as err:
print(err)
bpps = read_bpp_from_input_file(input_file,
expand_strand=False,
expand_orient=False)
bpps = read_bpp_from_input_file(input_file,
expand_strand=True,
expand_orient=True)
assert len(bpps) == 1
assert bpps[0].break2.strand == STRAND.POS
def test_unstranded_with_strand_calls(self):
fh = self.build_filehandle({
COLUMNS.break1_chromosome: '1',
COLUMNS.break1_position_start: 1,
COLUMNS.break1_position_end: 1,
COLUMNS.break1_strand: STRAND.POS,
COLUMNS.break1_orientation: ORIENT.RIGHT,
COLUMNS.break2_chromosome: '1',
COLUMNS.break2_position_start: 10,
COLUMNS.break2_position_end: 10,
COLUMNS.break2_strand: STRAND.NEG,
COLUMNS.break2_orientation: ORIENT.RIGHT,
COLUMNS.stranded: False,
COLUMNS.opposing_strands: True
})
bpps = read_bpp_from_input_file(fh, expand_strand=False, expand_orient=False)
self.assertEqual(1, len(bpps))
self.assertEqual(STRAND.NS, bpps[0].break1.strand)
self.assertEqual(STRAND.NS, bpps[0].break2.strand)
bpps = read_bpp_from_input_file(fh, expand_strand=False, expand_orient=True)
self.assertEqual(1, len(bpps))
self.assertEqual(STRAND.NS, bpps[0].break1.strand)
self.assertEqual(STRAND.NS, bpps[0].break2.strand)
fh = self.build_filehandle({
COLUMNS.break1_chromosome: '1',
COLUMNS.break1_position_start: 1,
COLUMNS.break1_position_end: 1,
COLUMNS.break1_strand: STRAND.POS,
COLUMNS.break1_orientation: ORIENT.RIGHT,
COLUMNS.break2_chromosome: '1',
COLUMNS.break2_position_start: 10,
COLUMNS.break2_position_end: 10,
COLUMNS.break2_strand: STRAND.NEG,
COLUMNS.break2_orientation: ORIENT.RIGHT,
COLUMNS.stranded: True,
COLUMNS.opposing_strands: True
})
bpps = read_bpp_from_input_file(fh, expand_strand=True, expand_orient=False)
self.assertEqual(1, len(bpps))
self.assertEqual(STRAND.POS, bpps[0].break1.strand)
self.assertEqual(STRAND.NEG, bpps[0].break2.strand)
bpps = read_bpp_from_input_file(fh, expand_strand=True, expand_orient=True)
self.assertEqual(1, len(bpps))
self.assertEqual(STRAND.POS, bpps[0].break1.strand)
self.assertEqual(STRAND.NEG, bpps[0].break2.strand)
def test_unstranded_with_strand_calls(self, tmp_path):
input_file = tmp_path / "inputs.tsv"
input_file.write_text(
mock_file_content({
COLUMNS.break1_chromosome: '1',
COLUMNS.break1_position_start: 1,
COLUMNS.break1_position_end: 1,
COLUMNS.break1_strand: STRAND.POS,
COLUMNS.break1_orientation: ORIENT.RIGHT,
COLUMNS.break2_chromosome: '1',
COLUMNS.break2_position_start: 10,
COLUMNS.break2_position_end: 10,
COLUMNS.break2_strand: STRAND.NEG,
COLUMNS.break2_orientation: ORIENT.RIGHT,
COLUMNS.stranded: False,
COLUMNS.opposing_strands: True,
}))
bpps = read_bpp_from_input_file(input_file,
expand_strand=False,
expand_orient=False)
assert len(bpps) == 1
assert bpps[0].break1.strand == STRAND.NS
assert bpps[0].break2.strand == STRAND.NS
input_file = tmp_path / "inputs2.tsv"
input_file.write_text(
mock_file_content({
COLUMNS.break1_chromosome: '1',
COLUMNS.break1_position_start: 1,
COLUMNS.break1_position_end: 1,
COLUMNS.break1_strand: STRAND.POS,
COLUMNS.break1_orientation: ORIENT.RIGHT,
COLUMNS.break2_chromosome: '1',
COLUMNS.break2_position_start: 10,
COLUMNS.break2_position_end: 10,
COLUMNS.break2_strand: STRAND.NEG,
COLUMNS.break2_orientation: ORIENT.RIGHT,
COLUMNS.stranded: True,
COLUMNS.opposing_strands: True,
}))
bpps = read_bpp_from_input_file(input_file,
expand_strand=True,
expand_orient=False)
assert len(bpps) == 1
assert bpps[0].break1.strand == STRAND.POS
assert bpps[0].break2.strand == STRAND.NEG
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_break2_strand_ns(self):
fh = self.build_filehandle({
COLUMNS.break1_chromosome: '1',
COLUMNS.break1_position_start: 1,
COLUMNS.break1_position_end: 1,
COLUMNS.break1_strand: STRAND.POS,
COLUMNS.break1_orientation: ORIENT.LEFT,
COLUMNS.break2_chromosome: '1',
COLUMNS.break2_position_start: 10,
COLUMNS.break2_position_end: 10,
COLUMNS.break2_strand: STRAND.NS,
COLUMNS.break2_orientation: ORIENT.RIGHT,
COLUMNS.stranded: True,
COLUMNS.opposing_strands: False
})
with self.assertRaises(NotSpecifiedError) as err:
print(err)
bpps = read_bpp_from_input_file(fh, expand_strand=False, expand_orient=False)
bpps = read_bpp_from_input_file(fh, expand_strand=True, expand_orient=True)
self.assertEqual(1, len(bpps))
self.assertEqual(STRAND.POS, bpps[0].break2.strand)
def run_main(self, inputfile, file_type, strand_specific=False):
outputfile = os.path.join(TEMP_OUTPUT, file_type + '.tab')
args = [
'mavis', SUBCOMMAND.CONVERT, '-o', outputfile, '-n', inputfile,
'--file_type', file_type, '--strand_specific', strand_specific
]
with patch.object(sys, 'argv', args):
self.assertEqual(0, main())
print('output', outputfile)
self.assertTrue(unique_exists(outputfile))
result = {}
for pair in read_bpp_from_input_file(outputfile):
result.setdefault(pair.tracking_id, []).append(pair)
return result
def test_pairing(self):
args = [
'mavis', SUBCOMMAND.PAIR, '-n',
os.path.join(DATA_PREFIX, 'pairing_annotations.tab'), '-o',
TEMP_OUTPUT, '--annotations',
os.path.join(DATA_PREFIX, 'pairing_reference_annotations_file.tab')
]
with patch.object(sys, 'argv', args):
self.assertEqual(0, main())
# make sure the output file exists
output = os.path.join(TEMP_OUTPUT, 'mavis_paired_A36971_A36973.tab')
self.assertTrue(os.path.exists(output))
# check that the expected pairings are present
bpps = read_bpp_from_input_file(output,
expand_strand=False,
expand_orient=False)
self.assertEqual(6, len(bpps))
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))
def test_break1_orient_ns(self):
fh = self.build_filehandle({
COLUMNS.break1_chromosome: '1',
COLUMNS.break1_position_start: 1,
COLUMNS.break1_position_end: 1,
COLUMNS.break1_strand: STRAND.POS,
COLUMNS.break1_orientation: ORIENT.NS,
COLUMNS.break2_chromosome: '1',
COLUMNS.break2_position_start: 10,
COLUMNS.break2_position_end: 10,
COLUMNS.break2_strand: STRAND.POS,
COLUMNS.break2_orientation: ORIENT.RIGHT,
COLUMNS.stranded: False,
COLUMNS.opposing_strands: False
})
bpps = read_bpp_from_input_file(fh, expand_strand=False, expand_orient=True)
self.assertEqual(1, len(bpps))
self.assertEqual(ORIENT.LEFT, bpps[0].break1.orient)
def run_main(self, inputfile, file_type, strand_specific=False):
outputfile = os.path.join(TEMP_OUTPUT, file_type + '.tab')
args = [
'mavis',
SUBCOMMAND.CONVERT,
'-o',
outputfile,
'-n',
inputfile,
'--file_type',
file_type,
'--strand_specific',
strand_specific,
]
with patch.object(sys, 'argv', args):
main()
print('output', outputfile)
assert glob_exists(outputfile, n=1)
result = {}
for pair in read_bpp_from_input_file(outputfile):
result.setdefault(pair.data['tracking_id'], []).append(pair)
return result
