def test_retrieve_af(self):
entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2', 'SVTYPE=BND;AF=0.2' ]
b1 = Bedpe(entry1)
self.assertEqual(b1.retrieve_af(), '0.2')
entry2 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND', 'SVTYPE=BND' ]
b2 = Bedpe(entry2)
self.assertIsNone(b2.retrieve_af())
def test_retrieve_svtype(self):
entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2', 'SVTYPE=BND;AF=0.2' ]
b1 = Bedpe(entry1)
self.assertEqual(b1.retrieve_svtype(), 'BND')
entry2 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'AF=0.2', 'AF=0.2' ]
with self.assertRaises(SystemExit):
b = Bedpe(entry2)
def test_adjust_by_tag(self):
entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2', 'SVTYPE=BND;AF=0.2' ]
b1 = Bedpe(entry1)
self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '+', 200), 200)
self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '-', 200), 201)
b1.info1 = 'SVTYPE=BND;AF=0.2;CIPOS=-2,3'
self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '-', 200), 203)
self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '+', 200), 202)
def test_parse_info_tag(self):
self.assertEqual(Bedpe.parse_info_tag('SVTYPE', 'SVTYPE'), True)
self.assertEqual(Bedpe.parse_info_tag('SVTYPE', 'AF='), False)
self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;AF=0.2', 'AF='),
'0.2')
self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;AF=0.2', 'SVTYPE='),
'BND')
self.assertEqual(
Bedpe.parse_info_tag('SVTYPE=BND;SECONDARY;AF=0.2', 'SECONDARY'),
True)
def test_adjust_by_ciend(self):
entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', 'SVTYPE=BND;AF=0.2', 'SVTYPE=BND;AF=0.2' ]
b1 = Bedpe(entry1)
self.assertEqual(self.converter.adjust_by_ciend(b1), 301)
b1.o2 = '+'
self.assertEqual(self.converter.adjust_by_ciend(b1), 300)
b1.info1 = 'SVTYPE=BND;AF=0.2;CIEND=-2,3'
self.assertEqual(self.converter.adjust_by_ciend(b1), 302)
b1.o2 = '-'
self.assertEqual(self.converter.adjust_by_ciend(b1), 303)
def test__combine_sname_values(self):
self.assertEqual(
set(
Bedpe._combine_sname_values('sample1:2',
'sample2:4,sample3:5').split(',')),
set(['sample1:2', 'sample2:4', 'sample3:5']))
self.assertEqual(
Bedpe._combine_sname_values(None, 'sample2:4,sample3:5'),
'sample2:4,sample3:5')
self.assertEqual(
Bedpe._combine_sname_values('sample2:4,sample3:5', None),
'sample2:4,sample3:5')
def test_adjust_by_cipos(self):
entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', 'SVTYPE=BND;AF=0.2', 'SVTYPE=BND;AF=0.2' ]
b1 = Bedpe(entry1)
self.assertEqual(b1.b1, 200)
b1.o1 = '-'
b1.adjust_by_cipos()
self.assertEqual(b1.b1, 201)
b1.misc[0] = 'SVTYPE=BND;AF=0.2;CIPOS=-2,3'
b1.adjust_by_cipos()
self.assertEqual(b1.b1, 203)
b1.o1 = '+'
b1.adjust_by_cipos()
self.assertEqual(b1.b1, 202)
def test_sname_value(self):
self.assertEqual(Bedpe.sname_value('SNAME=sample1:2,sample2:3'),
'sample1:2,sample2:3')
self.assertIsNone(Bedpe.sname_value('AF'))
self.assertIsNone(Bedpe.sname_value('SNAME='))
self.assertEqual(
Bedpe.sname_value(
'SNAME1=older_sample1:2,older_sample2:2;SNAME=sample1:2,sample2:3'
), 'sample1:2,sample2:3')
self.assertEqual(
Bedpe.sname_value(
'SNAME1=older_sample 1:2,older_sample2:2;SNAME=sample1:2,sample2:3;AF=1'
), 'sample1:2,sample2:3')
def test_adjust_by_ciend(self):
entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', 'SVTYPE=BND;AF=0.2', 'SVTYPE=BND;AF=0.2' ]
b1 = Bedpe(entry1)
self.assertEqual(b1.b2, 301)
b1.o2 = '+'
b1.adjust_by_ciend()
self.assertEqual(b1.b2, 300)
b1.misc[0] = 'SVTYPE=BND;AF=0.2;CIEND=-2,3'
b1.adjust_by_ciend()
self.assertEqual(b1.b2, 302)
b1.o2 = '-'
b1.adjust_by_ciend()
self.assertEqual(b1.b2, 303)
def test_retrieve_svtype(self):
entry1 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2',
'SVTYPE=BND;AF=0.2'
]
b1 = Bedpe(entry1)
self.assertEqual(b1.retrieve_svtype(), 'BND')
entry2 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'AF=0.2', 'AF=0.2'
]
with self.assertRaises(SystemExit):
b = Bedpe(entry2)
def test__update_sname_field(self):
expected = set(['sample 2:4', 'sample3:12'])
result = Bedpe._update_sname_field('SNAME=sample 2:4', 'SNAME=sample3:12')
tag_name, values = result.split('=')
self.assertEqual(tag_name, 'SNAME')
result_set = set(values.split(','))
self.assertEqual(result_set, expected)
# Test to ensure we don't fail if no SNAME is present
result2 = Bedpe._update_sname_field('AF=0.5', 'AF=0.1')
self.assertEqual(result2, 'AF=0.5')
# Test if the first sample is missing SNAME
result2 = Bedpe._update_sname_field('AF=0.5', 'AF=0.1;SNAME=sample5:12')
self.assertEqual(result2, 'AF=0.5;SNAME=sample5:12')
def cluster_bedpe(self, in_file, bedpe_out, is_sorted):
# Locally alias instance variables
max_distance = self.max_distance
eval_param = self.eval_param
in_header = True
for line in in_file:
if line.startswith('#') and in_header:
if line.startswith('#CHROM'):
bedpe_out.write('##INFO=<ID=RETAINED,Number=0,Type=Flag,Description="Variants clustering with this call were pruned">\n')
bedpe_out.write(line)
continue
in_header = False
self.bedpe_lines += 1
bedpe = Bedpe(line.rstrip().split('\t'))
if bedpe.af is None:
sys.stderr.write('No allele frequency for variant found. This tool requires allele frequency information to function. Please add with svtools afreq and rerun\n')
sys.exit(1)
if bedpe.af == '.':
self.skipped_lines += 1
continue
matched_clusters = []
for cluster in self.cluster_list:
if cluster.can_add(bedpe, max_distance):
cluster.add(bedpe, eval_param)
matched_clusters.append(cluster)
if not matched_clusters:
new_cluster = Cluster()
new_cluster.add(bedpe, eval_param)
self.cluster_list.append(new_cluster)
else:
if len(matched_clusters) > 1:
i = 0
pruned_clusters = []
while i < (len(matched_clusters) - 1):
j = i + 1
to_delete = set()
while j < len(matched_clusters):
if matched_clusters[i].can_add(matched_clusters[j].elements[0], max_distance):
matched_clusters[i].add(matched_clusters[j].elements[0], eval_param)
pruned_clusters.append(matched_clusters[j])
to_delete.add(j)
j += 1
for index in sorted(to_delete, reverse=True):
del matched_clusters[index]
i += 1
if pruned_clusters:
self.cluster_list = [cluster for cluster in self.cluster_list if cluster not in pruned_clusters]
#prune and print eligible clusters
if self.bedpe_lines % 1000 == 0 and is_sorted:
self.cluster_list = self.prune(bedpe,
False,
bedpe_out)
self.cluster_list = self.prune(None,
True,
bedpe_out)
sys.stderr.write(self.stats_report_string())
return
def test_adjust_by_tag(self):
entry1 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2',
'SVTYPE=BND;AF=0.2'
]
b1 = Bedpe(entry1)
self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '+', 200),
200)
self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '-', 200),
201)
b1.info1 = 'SVTYPE=BND;AF=0.2;CIPOS=-2,3'
self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '-', 200),
203)
self.assertEqual(self.converter.adjust_by_tag(b1, 'CIPOS', '+', 200),
202)
def test__update_sname_field(self):
expected = set(['sample2:4', 'sample3:12'])
result = Bedpe._update_sname_field('SNAME=sample2:4', 'SNAME=sample3:12')
tag_name, values = result.split('=')
self.assertEqual(tag_name, 'SNAME')
result_set = set(values.split(','))
self.assertEqual(result_set, expected)
def bedpeToVcf(bedpe_file, vcf_out):
myvcf = Vcf()
converter = BedpeToVcfConverter(myvcf)
in_header = True
# parse the bedpe data
header = list()
for line in bedpe_file:
if in_header:
if line[0:2] == '##':
header.append(line)
continue
elif line[0] == '#' and line[1] != '#':
sample_list_str = line.rstrip().split('\t', 20)[-1]
header.append('\t'.join([
'#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER',
'INFO', sample_list_str
]))
continue
else:
in_header = False
myvcf.add_header(header)
myvcf.file_format = 'VCFv4.2'
vcf_out.write(myvcf.get_header() + '\n')
#
bedpe = Bedpe(line.rstrip().split('\t'))
variants = converter.convert(bedpe)
for v in variants:
vcf_out.write(v.get_var_string() + '\n')
# close the VCF output file
vcf_out.close()
return
def test_malformed(self):
entry1 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'MISSING',
'SVTYPE=BND;AF=0.2'
]
b1 = Bedpe(entry1)
self.assertEqual(b1.malformedFlag, 1)
entry2 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2',
'MISSING'
]
b2 = Bedpe(entry2)
self.assertEqual(b2.malformedFlag, 2)
self.assertEqual(b2.info1, entry2[18])
def test__update_sname_field(self):
expected = set(['sample2:4', 'sample3:12'])
result = Bedpe._update_sname_field('SNAME=sample2:4',
'SNAME=sample3:12')
tag_name, values = result.split('=')
self.assertEqual(tag_name, 'SNAME')
result_set = set(values.split(','))
self.assertEqual(result_set, expected)
def test__update_sname_field(self):
expected = set(['sample 2:4', 'sample3:12'])
result = Bedpe._update_sname_field('SNAME=sample 2:4',
'SNAME=sample3:12')
tag_name, values = result.split('=')
self.assertEqual(tag_name, 'SNAME')
result_set = set(values.split(','))
self.assertEqual(result_set, expected)
# Test to ensure we don't fail if no SNAME is present
result2 = Bedpe._update_sname_field('AF=0.5', 'AF=0.1')
self.assertEqual(result2, 'AF=0.5')
# Test if the first sample is missing SNAME
result2 = Bedpe._update_sname_field('AF=0.5',
'AF=0.1;SNAME=sample5:12')
self.assertEqual(result2, 'AF=0.5;SNAME=sample5:12')
def test_parse_info_tag(self):
self.assertEqual(Bedpe.update_info_tag('SNAME=sample', 'SNAME=', 'sample,sample2'), 'SNAME=sample,sample2')
self.assertEqual(Bedpe.update_info_tag('SNAME=sample;AF=0.75', 'SNAME=', 'sample,sample2'), 'SNAME=sample,sample2;AF=0.75')
with self.assertRaises(ValueError):
Bedpe.update_info_tag('AF=0.75', 'SNAME=', 'sample,sample2')
with self.assertRaises(ValueError):
Bedpe.update_info_tag('SECONDARY;AF=0.5', 'SECONDARY', 'NEW_VALUE')
with self.assertRaises(ValueError):
Bedpe.update_info_tag('AF=0.5;SECONDARY', 'SECONDARY', 'NEW_VALUE')
def test_str(self):
# Note that we are testing float to float equivalence. Actually passing in an integer will result in it being converted to float with
# with decimal place
entry1 = [
'1', '200', '300', '2', '300', '400', '777_1', '57.0', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2',
'SVTYPE=BND;AF=0.2'
]
b1 = Bedpe(entry1)
self.assertEqual(str(b1), '\t'.join(entry1))
def cluster_bedpe(self, in_file, bedpe_out, is_sorted):
# Locally alias instance variables
max_distance = self.max_distance
eval_param = self.eval_param
in_header = True
for line in in_file:
if line.startswith('#') and in_header:
bedpe_out.write(line)
continue
in_header = False
self.bedpe_lines += 1
bedpe = Bedpe(line.rstrip().split('\t'))
if bedpe.af is None:
sys.stderr.write('No allele frequency for variant found. This tool requires allele frequency information to function. Please add with svtools afreq and rerun\n')
sys.exit(1)
if bedpe.af == '.':
self.skipped_lines += 1
continue
matched_clusters = []
for cluster in self.cluster_list:
if cluster.can_add(bedpe, max_distance):
cluster.add(bedpe, eval_param)
matched_clusters.append(cluster)
if not matched_clusters:
new_cluster = Cluster()
new_cluster.add(bedpe, eval_param)
self.cluster_list.append(new_cluster)
else:
if len(matched_clusters) > 1:
i = 0
matched_cluster_pruned = False
while i < (len(matched_clusters) - 1):
j = i + 1
while j < len(matched_clusters):
if matched_clusters[i].can_add(matched_clusters[j].elements[0], max_distance):
matched_clusters[i].add(matched_clusters[j].elements[0], eval_param)
matched_cluster_pruned = True
del matched_clusters[j]
j += 1
i += 1
if matched_cluster_pruned:
self.cluster_list = [cluster for cluster in self.cluster_list if cluster not in matched_clusters]
#prune and print eligible clusters
if self.bedpe_lines % 1000 == 0 and is_sorted:
self.cluster_list = self.prune(bedpe,
False,
bedpe_out)
self.cluster_list = self.prune(None,
True,
bedpe_out)
sys.stderr.write(self.stats_report_string())
return
def test_add(self):
bedpe1 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'MISSING',
'SVTYPE=BND;AF=0.2'
]
b1 = Bedpe(bedpe1)
bedpe2 = [
'1', '195', '305', '2', '295', '405', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'MISSING',
'SVTYPE=BND;AF=0.3'
]
b2 = Bedpe(bedpe2)
c = Cluster()
c.add(b1, None)
self.assertEqual(c.size, 1)
self.assertEqual(c.sv_event, 'BND')
self.assertEqual(c.filter, '0.2')
self.assertEqual(c.chrom_a, '1')
self.assertEqual(c.min_a, 200)
self.assertEqual(c.max_a, 300)
self.assertEqual(c.chrom_b, '2')
self.assertEqual(c.min_b, 300)
self.assertEqual(c.max_b, 400)
self.assertEqual(c.strand_a, '+')
self.assertEqual(c.strand_b, '-')
c.add(b2, None)
self.assertEqual(c.size, 2)
self.assertEqual(c.sv_event, 'BND')
self.assertEqual(c.filter, '0.3')
self.assertEqual(c.chrom_a, '1')
self.assertEqual(c.min_a, 195)
self.assertEqual(c.max_a, 305)
self.assertEqual(c.chrom_b, '2')
self.assertEqual(c.min_b, 295)
self.assertEqual(c.max_b, 405)
self.assertEqual(c.strand_a, '+')
self.assertEqual(c.strand_b, '-')
def processBEDPE(bedpe_stream, name, dist, output_handle):
#Process the BEDPE file and convert each entry to SAM.
converter = BedpetoBlockedBedConverter(name, dist)
output_handle.write(converter.track_name())
for line in bedpe_stream:
# ignore header
if line[0] == "#":
continue
lineList = line.rstrip().split('\t')
if lineList:
bedpe = Bedpe(lineList)
output_handle.write('\n'.join(converter.convert(bedpe)) + '\n')
def test_parse_info_tag(self):
self.assertEqual(Bedpe.parse_info_tag('SVTYPE', 'SVTYPE'), True)
self.assertEqual(Bedpe.parse_info_tag('SVTYPE', 'AF='), False)
self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;AF=0.2', 'AF='), '0.2')
self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;AF=0.2', 'SVTYPE='), 'BND')
self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;SECONDARY;AF=0.2', 'SECONDARY'), True)
self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;SECONDARY;BAD_AF=0.3;AF=0.2', 'AF='), '0.2')
def test_parse_info_tag(self):
self.assertEqual(
Bedpe.update_info_tag('SNAME=sample', 'SNAME=', 'sample,sample2'),
'SNAME=sample,sample2')
self.assertEqual(
Bedpe.update_info_tag('SNAME=sample;AF=0.75', 'SNAME=',
'sample,sample2'),
'SNAME=sample,sample2;AF=0.75')
with self.assertRaises(ValueError):
Bedpe.update_info_tag('AF=0.75', 'SNAME=', 'sample,sample2')
with self.assertRaises(ValueError):
Bedpe.update_info_tag('SECONDARY;AF=0.5', 'SECONDARY', 'NEW_VALUE')
with self.assertRaises(ValueError):
Bedpe.update_info_tag('AF=0.5;SECONDARY', 'SECONDARY', 'NEW_VALUE')
def test_can_add(self):
bedpe = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'MISSING',
'SVTYPE=BND;AF=0.2'
]
b = Bedpe(bedpe)
c = Cluster()
c.chrom_a = b.c1
c.chrom_b = b.c2
c.min_a = b.s1
c.max_a = b.e1
c.min_b = b.s2
c.max_b = b.e2
c.strand_a = b.o1
c.strand_b = b.o2
self.assertTrue(c.can_add(b, 1))
c.size = 1
c.sv_event = 'DEL'
self.assertFalse(c.can_add(b, 1))
c.sv_event = 'BND'
self.assertTrue(c.can_add(b, 1))
c.chrom_a = 'X'
self.assertFalse(c.can_add(b, 1))
c.chrom_a = b.c1
c.chrom_b = 'X'
self.assertFalse(c.can_add(b, 1))
c.chrom_b = b.c2
c.min_a = 305
self.assertFalse(c.can_add(b, 1))
c.min_a = b.s1
c.max_a = 150
self.assertFalse(c.can_add(b, 1))
c.max_a = b.e1
c.min_b = 405
self.assertFalse(c.can_add(b, 1))
c.min_b = b.s1
c.max_b = 150
self.assertFalse(c.can_add(b, 1))
def test_get_cluster_string(self):
bedpe = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'MISSING',
'SVTYPE=BND;AF=0.2'
]
b = Bedpe(bedpe)
c = Cluster()
with self.assertRaises(ValueError):
c.get_cluster_string()
c.add(b, None)
self.assertEqual(c.get_cluster_string(), str(b))
def test_info(self):
entry1 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'MISSING',
'SVTYPE=BND;AF=0.2'
]
b1 = Bedpe(entry1)
self.assertEqual(b1.info, 'SVTYPE=BND;AF=0.2')
entry2 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2',
'MISSING'
]
b2 = Bedpe(entry2)
self.assertEqual(b2.info, 'SVTYPE=BND;AF=0.2')
entry3 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2',
'SECONDARY'
]
b3 = Bedpe(entry3)
self.assertEqual(b3.info, 'SVTYPE=BND;AF=0.2')
def test_retrieve_af(self):
entry1 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2',
'SVTYPE=BND;AF=0.2'
]
b1 = Bedpe(entry1)
self.assertEqual(b1.retrieve_af(), '0.2')
entry2 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND',
'SVTYPE=BND'
]
b2 = Bedpe(entry2)
self.assertIsNone(b2.retrieve_af())
entry3 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.',
'SVTYPE=BND;AF=0.2;FIN_AF=0.01', 'SVTYPE=BND;AF=0.2;FIN_AF=0.01'
]
b3 = Bedpe(entry3)
self.assertEqual(b3.retrieve_af(), '0.2')
def test_parse_score(self):
self.assertEqual(Bedpe.parse_score('20'), 20)
self.assertEqual(Bedpe.parse_score('.'), '.')
def flag_as_pruned(bedpe):
'''
Mark a BEDPE info field(s) as RETAINED
'''
if not Bedpe.parse_info_tag(bedpe.info, 'RETAINED'):
bedpe.set_info('RETAINED', None)
def flag_as_pruned(bedpe):
'''
Mark a BEDPE info field(s) as RETAINED
'''
if not Bedpe.parse_info_tag(bedpe.info, 'RETAINED'):
bedpe.set_info('RETAINED', None)
def test_parse_score(self):
self.assertEqual(Bedpe.parse_score('20'), 20)
self.assertEqual(Bedpe.parse_score('.'), '.')
def test_set_info(self):
entry1 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'MISSING',
'SVTYPE=BND'
]
b1 = Bedpe(entry1)
b1.set_info('AF', '0.2')
self.assertEqual(b1.info, 'SVTYPE=BND;AF=0.2')
entry2 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND',
'MISSING'
]
b2 = Bedpe(entry2)
b2.set_info('AF', '0.2')
self.assertEqual(b2.info, 'SVTYPE=BND;AF=0.2')
entry3 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND',
'SECONDARY'
]
b3 = Bedpe(entry3)
b3.set_info('AF', '0.2')
self.assertEqual(b3.info1, 'SVTYPE=BND;AF=0.2')
self.assertEqual(b3.info2, 'SECONDARY;AF=0.2')
entry4 = [
'1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND', '.'
]
b4 = Bedpe(entry4)
b4.set_info('PRESENT', None)
self.assertEqual(b4.info, 'SVTYPE=BND;PRESENT')
self.assertEqual(b4.info2, '.')
def varLookup(aFile, bFile, bedpe_out, max_distance, pass_prefix, cohort_name):
# FIXME The following code is heavily duplicated with vcftobedpe and bedpetovcf. Harmonize!!!
bList = list()
headerObj = Vcf() #co-opt the VCF header object
if cohort_name is None:
cohort_name = str(str(bFile).split('/')[-1])
if bFile == "stdin":
bData = sys.stdin
elif bFile.endswith('.gz'):
bData = gzip.open(bFile, 'rb')
else:
bData = open(bFile, 'r')
for bLine in bData:
if bLine.startswith(pass_prefix):
continue
bentry = Bedpe(bLine.rstrip().split('\t'))
if bentry.af is None:
sys.stderr.write(
'No allele frequency for variant found in -b file. This tool requires allele frequency information to function. Please add with svtools afreq and rerun\n'
)
sys.exit(1)
bList.append(bentry)
if aFile == "stdin":
aData = sys.stdin
elif aFile.endswith('.gz'):
aData = gzip.open(aFile, 'rb')
else:
aData = open(aFile, 'r')
in_header = True
header_lines = []
sample_list = None
for aLine in aData:
if pass_prefix is not None and aLine.startswith(pass_prefix):
if aLine[0] == '#' and aLine[1] != '#':
sample_list = aLine.rstrip().split('\t', 14)[-1]
else:
header_lines.append(aLine)
continue
else:
if in_header == True:
headerObj.add_header(header_lines)
headerObj.add_info(
cohort_name + '_AF', '.', 'Float',
'Allele frequency(ies) for matching variants found in the '
+ cohort_name + ' vcf' + ' (' +
str(str(bFile).split('/')[-1]) + ')')
headerObj.add_info(
cohort_name + '_VarID', '.', 'Integer',
'List of Variant ID(s) for matching variants found in the '
+ cohort_name + ' vcf' + ' (' +
str(str(bFile).split('/')[-1]) + ')')
header = headerObj.get_header()
bedpe_out.write(header[:header.rfind('\n')] + '\n')
if len(sample_list) > 0:
bedpe_out.write('\t'.join([
'#CHROM_A', 'START_A', 'END_A', 'CHROM_B', 'START_B',
'END_B', 'ID', 'QUAL', 'STRAND_A', 'STRAND_B', 'TYPE',
'FILTER', 'INFO_A', 'INFO_B', sample_list
]) + '\n')
else:
bedpe_out.write('\t'.join([
'#CHROM_A', 'START_A', 'END_A', 'CHROM_B', 'START_B',
'END_B', 'ID', 'QUAL', 'STRAND_A', 'STRAND_B', 'TYPE',
'FILTER', 'INFO_A', 'INFO_B'
]) + '\n')
in_header = False
a = Bedpe(aLine.rstrip().split('\t'))
if a.af is None:
sys.stderr.write(
'No allele frequency for variant found in -a file. This tool requires allele frequency information to function. Please add with svtools afreq and rerun\n'
)
sys.exit(1)
for b in bList:
add(a, b, max_distance)
bedpe_out.write(get_var_string(a, cohort_name) + '\n')
def test__combine_sname_values(self):
self.assertEqual(set(Bedpe._combine_sname_values('sample1:2', 'sample2:4,sample3:5').split(',')), set(['sample1:2', 'sample2:4', 'sample3:5']))
self.assertEqual(Bedpe._combine_sname_values(None, 'sample2:4,sample3:5'), 'sample2:4,sample3:5')
self.assertEqual(Bedpe._combine_sname_values('sample2:4,sample3:5', None), 'sample2:4,sample3:5')
def convert(self, primary_variant, secondary_variant=None):
'''
Convert the passed VCF variant(s) into a BEDPE object
'''
vcf_variant = primary_variant
if primary_variant is None:
vcf_variant = secondary_variant
try:
sv_type = vcf_variant.info['SVTYPE']
except KeyError:
raise ValueError('SVTYPE field required for conversion to BEDPE')
parser = self.simple_breakpoints
if sv_type == 'BND':
parser = self.bnd_breakpoints
c1, s1, e1, c2, s2, e2, o1, o2 = parser(vcf_variant)
s1, e1 = self.adjust_coordinate(vcf_variant, 'CIPOS', s1, e1)
s2, e2 = self.adjust_coordinate(vcf_variant, 'CIEND', s2, e2)
orig_name_a = vcf_variant.var_id
orig_ref_a = vcf_variant.ref
orig_alt_a = vcf_variant.alt
info_a = vcf_variant.get_info_string()
if primary_variant is None:
info_a = "MISSING"
orig_name_a = orig_ref_a = orig_alt_a = '.'
c1, s1, e1, o1, c2, s2, e2, o2 = c2, s2, e2, o2, c1, s1, e1, o1
info_b = '.'
orig_name_b = orig_ref_b = orig_alt_b = '.'
if sv_type == 'BND':
if secondary_variant is None:
info_b = "MISSING"
else:
info_b = secondary_variant.get_info_string()
orig_name_b = secondary_variant.var_id
orig_ref_b = secondary_variant.ref
orig_alt_b = secondary_variant.alt
sc1, ss1, se1, sc2, ss2, se2, so1, so2 = parser(
secondary_variant)
s2, e2 = self.adjust_coordinate(secondary_variant, 'CIPOS',
ss1, se1)
# For MANTA single-ended BNDs, EVENT is not present.
# XXX This has probably already been calculated outside of this method. May be a candidate to memoize or otherwise cache?
# By adding to the variant class, perhaps?
name = vcf_variant.var_id
if 'EVENT' in vcf_variant.info:
name = vcf_variant.info['EVENT']
elif 'MATEID' in vcf_variant.info and vcf_variant.var_id.startswith(
'Manta'):
# Specifically handle Manta
name, end = vcf_variant.var_id.rsplit(':', 1)
fields = map(str, [
c1,
max(s1, 0),
max(e1, 0),
c2,
max(s2, 0),
max(e2, 0),
name,
vcf_variant.qual,
o1,
o2,
sv_type,
vcf_variant.filter,
orig_name_a,
orig_ref_a,
orig_alt_a,
orig_name_b,
orig_ref_b,
orig_alt_b,
info_a,
info_b,
])
if vcf_variant.get_format_string() is not None:
fields += [
vcf_variant.get_format_string(),
vcf_variant.get_gt_string()
]
return Bedpe(fields)
def test_sname_value(self):
self.assertEqual(Bedpe.sname_value('SNAME=sample1:2,sample2:3'), 'sample1:2,sample2:3')
self.assertIsNone(Bedpe.sname_value('AF'))
self.assertIsNone(Bedpe.sname_value('SNAME='))
def test_set_info(self):
entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'MISSING', 'SVTYPE=BND' ]
b1 = Bedpe(entry1)
b1.set_info('AF', '0.2')
self.assertEqual(b1.info, 'SVTYPE=BND;AF=0.2')
entry2 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND', 'MISSING' ]
b2 = Bedpe(entry2)
b2.set_info('AF', '0.2')
self.assertEqual(b2.info, 'SVTYPE=BND;AF=0.2')
entry3 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND', 'SECONDARY' ]
b3 = Bedpe(entry3)
b3.set_info('AF', '0.2')
self.assertEqual(b3.info1, 'SVTYPE=BND;AF=0.2')
self.assertEqual(b3.info2, 'SECONDARY;AF=0.2')
entry4 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND', '.' ]
b4 = Bedpe(entry4)
b4.set_info('PRESENT', None)
self.assertEqual(b4.info, 'SVTYPE=BND;PRESENT')
self.assertEqual(b4.info2, '.')
