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
class TestBedpeToVcfConverter(TestCase):
def setUp(self):
vcf = Vcf()
self.converter = BedpeToVcfConverter(vcf)
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_determine_sep(self):
self.assertEqual(self.converter.determine_sep('-'), '[')
self.assertEqual(self.converter.determine_sep('+'), ']')
def test_determine_flanks(self):
self.assertEqual(self.converter.determine_flanks('-'), ('', 'N'))
self.assertEqual(self.converter.determine_flanks('+'), ('N', ''))
def test_bnd_alt_string(self):
self.assertEqual(self.converter.bnd_alt_string('+', '-', '2', '22222'), 'N[2:22222[')
self.assertEqual(self.converter.bnd_alt_string('-', '+', '2', '22222'), ']2:22222]N')
class TestBedpeToVcfConverter(TestCase):
def setUp(self):
vcf = Vcf()
self.converter = BedpeToVcfConverter(vcf)
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_determine_sep(self):
self.assertEqual(self.converter.determine_sep('-'), '[')
self.assertEqual(self.converter.determine_sep('+'), ']')
def test_determine_flanks(self):
self.assertEqual(self.converter.determine_flanks('-'), ('', 'N'))
self.assertEqual(self.converter.determine_flanks('+'), ('N', ''))
def test_bnd_alt_string(self):
self.assertEqual(self.converter.bnd_alt_string('+', '-', '2', '22222'),
'N[2:22222[')
self.assertEqual(self.converter.bnd_alt_string('-', '+', '2', '22222'),
']2:22222]N')
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 and header if no variants found
if in_header == True:
myvcf.add_header(header)
myvcf.file_format='VCFv4.2'
vcf_out.write(myvcf.get_header() + '\n')
vcf_out.close()
return
def setUp(self):
vcf = Vcf()
self.converter = BedpeToVcfConverter(vcf)
def setUp(self):
vcf = Vcf()
self.converter = BedpeToVcfConverter(vcf)
