def vcfToBedpe(vcf_file, bedpe_out):
converter = VcfToBedpeConverter()
vcf = svtools.vcf.file.Vcf()
in_header = True
header = []
sample_list = []
bnds = dict()
sec_bnds = dict()
v = []
for line in vcf_file:
if in_header:
if line[0:2] == '##':
if line.split('=')[0] == '##fileformat':
line = '##fileformat=' + "BEDPE" + '\n'
if line.split('=')[0] == '##fileDate':
line = '##fileDate=' + time.strftime('%Y%m%d') + '\n'
header.append(line)
continue
elif line[0] == '#' and line[1] != '#':
sample_list = line.rstrip().split('\t')[9:]
header.append(line)
continue
else:
# print header
in_header = False
vcf.add_header(header)
if "SVTYPE" in [info.id for info in vcf.info_list]:
vcf.add_info_after("SVTYPE", "POS", 1, 'Integer', 'Position of the variant described in this record')
header=vcf.get_header()
bedpe_out.write(header[:header.rfind('\n')] + '\n')
final_header_line = ['#CHROM_A',
'START_A',
'END_A',
'CHROM_B',
'START_B',
'END_B',
'ID',
'QUAL',
'STRAND_A',
'STRAND_B',
'TYPE',
'FILTER',
'NAME_A',
'REF_A',
'ALT_A',
'NAME_B',
'REF_B',
'ALT_B',
'INFO_A',
'INFO_B']
if len(sample_list) > 0:
bedpe_out.write('\t'.join(final_header_line + ['FORMAT','\t'.join(map(str,sample_list))]) + '\n')
else:
bedpe_out.write('\t'.join(final_header_line) + '\n')
v = line.rstrip().split('\t')
var = svtools.vcf.variant.Variant(v, vcf)
var.set_info("POS", var.pos)
unique_name = var.var_id
# The EVENT ID is not unique. Stick with ID column.
# if 'EVENT' in var.info:
# unique_name = var.info['EVENT']
if var.info['SVTYPE'] != 'BND':
bedpe_out.write(str(converter.convert(var)) + '\n')
else:
# Manta doesn't use the SECONDARY flag
# So, just check whether the mate ID is in bnds
# Which means that the mate has already been seen
if 'MATEID' in var.info:
mate_id = var.info['MATEID']
if mate_id in bnds:
var1 = bnds[mate_id]
bedpe_out.write(str(converter.convert(var1, var)) + '\n')
del bnds[mate_id]
else:
bnds.update({unique_name:var})
else:
bnds.update({unique_name:var})
continue
intersected_keys = bnds.viewkeys() & sec_bnds.viewkeys()
for key in intersected_keys:
bedpe_out.write(str(converter.convert(bnds[key], sec_bnds[key])) + '\n')
del bnds[key]
del sec_bnds[key]
if bnds is not None:
for bnd in bnds:
sys.stderr.write('Warning: missing secondary multiline variant at ID:' + bnd + '\n')
bedpe_out.write(str(converter.convert(bnds[bnd], None)) + '\n')
if sec_bnds is not None:
for bnd in sec_bnds:
sys.stderr.write('Warning: missing primary multiline variant at ID:' + bnd + '\n')
bedpe_out.write(str(converter.convert(None, sec_bnds[bnd])) + '\n')
# close the files
bedpe_out.close()
return
def vcfToBedpe(vcf_file, bedpe_out):
converter = VcfToBedpeConverter()
vcf = svtools.vcf.file.Vcf()
in_header = True
header = []
sample_list = []
bnds = dict()
sec_bnds = dict()
v = []
for line in vcf_file:
if in_header:
if line[0:2] == '##':
if line.split('=')[0] == '##fileformat':
line = '##fileformat=' + "BEDPE" + '\n'
if line.split('=')[0] == '##fileDate':
line = '##fileDate=' + time.strftime('%Y%m%d') + '\n'
header.append(line)
continue
elif line[0] == '#' and line[1] != '#':
sample_list = line.rstrip().split('\t')[9:]
header.append(line)
continue
else:
# print header
in_header = False
vcf.add_header(header)
if "SVTYPE" in [info.id for info in vcf.info_list]:
vcf.add_info_after(
"SVTYPE", "POS", 1, 'Integer',
'Position of the variant described in this record')
header = vcf.get_header()
bedpe_out.write(header[:header.rfind('\n')] + '\n')
final_header_line = [
'#CHROM_A', 'START_A', 'END_A', 'CHROM_B', 'START_B',
'END_B', 'ID', 'QUAL', 'STRAND_A', 'STRAND_B', 'TYPE',
'FILTER', 'NAME_A', 'REF_A', 'ALT_A', 'NAME_B', 'REF_B',
'ALT_B', 'INFO_A', 'INFO_B'
]
if len(sample_list) > 0:
bedpe_out.write('\t'.join(
final_header_line +
['FORMAT', '\t'.join(map(str, sample_list))]) + '\n')
else:
bedpe_out.write('\t'.join(final_header_line) + '\n')
v = line.rstrip().split('\t')
var = svtools.vcf.variant.Variant(v, vcf)
var.set_info("POS", var.pos)
# If there is no MATEID then assume this is a single-ended BND and simply output
if var.info['SVTYPE'] != 'BND' or 'MATEID' not in var.info:
bedpe_out.write(str(converter.convert(var)) + '\n')
else:
mate_id = var.info['MATEID']
if 'SECONDARY' in var.info:
if mate_id in bnds:
#primary
var1 = bnds[mate_id]
bedpe_out.write(str(converter.convert(var1, var)) + '\n')
del bnds[mate_id]
else:
sec_bnds.update({var.var_id: var})
else:
if mate_id in sec_bnds:
var2 = sec_bnds[mate_id]
bedpe_out.write(str(converter.convert(var, var2)) + '\n')
del sec_bnds[mate_id]
elif mate_id in bnds:
var1 = bnds[mate_id]
bedpe_out.write(str(converter.convert(var1, var)) + '\n')
del bnds[mate_id]
else:
bnds.update({var.var_id: var})
if bnds is not None:
for bnd in bnds:
sys.stderr.write(
'Warning: missing secondary multiline variant at ID:' + bnd +
'\n')
bedpe_out.write(str(converter.convert(bnds[bnd], None)) + '\n')
if sec_bnds is not None:
for bnd in sec_bnds:
sys.stderr.write(
'Warning: missing primary multiline variant at ID:' + bnd +
'\n')
bedpe_out.write(str(converter.convert(None, sec_bnds[bnd])) + '\n')
# close the files
bedpe_out.close()
return
def vcfToBedpe(vcf_file, bedpe_out):
converter = VcfToBedpeConverter()
vcf = svtools.vcf.file.Vcf()
in_header = True
header = []
sample_list = []
bnds = dict()
sec_bnds = dict()
v = []
for line in vcf_file:
if in_header:
if line[0:2] == '##':
if line.split('=')[0] == '##fileformat':
line = '##fileformat=' + "BEDPE" + '\n'
if line.split('=')[0] == '##fileDate':
line = '##fileDate=' + time.strftime('%Y%m%d') + '\n'
header.append(line)
continue
elif line[0] == '#' and line[1] != '#':
sample_list = line.rstrip().split('\t')[9:]
header.append(line)
continue
else:
# print header
in_header = False
vcf.add_header(header)
if "SVTYPE" in [info.id for info in vcf.info_list]:
vcf.add_info_after("SVTYPE", "POS", 1, 'Integer', 'Position of the variant described in this record')
header=vcf.get_header()
bedpe_out.write(header[:header.rfind('\n')] + '\n')
final_header_line = ['#CHROM_A',
'START_A',
'END_A',
'CHROM_B',
'START_B',
'END_B',
'ID',
'QUAL',
'STRAND_A',
'STRAND_B',
'TYPE',
'FILTER',
'NAME_A',
'REF_A',
'ALT_A',
'NAME_B',
'REF_B',
'ALT_B',
'INFO_A',
'INFO_B']
if len(sample_list) > 0:
bedpe_out.write('\t'.join(final_header_line + ['FORMAT','\t'.join(map(str,sample_list))]) + '\n')
else:
bedpe_out.write('\t'.join(final_header_line) + '\n')
v = line.rstrip().split('\t')
var = svtools.vcf.variant.Variant(v, vcf)
var.set_info("POS", var.pos)
# If there is no MATEID then assume this is a single-ended BND and simply output
if var.info['SVTYPE'] != 'BND' or 'MATEID' not in var.info:
bedpe_out.write(str(converter.convert(var)) + '\n')
else:
mate_id = var.info['MATEID']
if 'SECONDARY' in var.info:
if mate_id in bnds:
#primary
var1 = bnds[mate_id]
bedpe_out.write(str(converter.convert(var1, var)) + '\n')
del bnds[mate_id]
else:
sec_bnds.update({var.var_id:var})
else:
if mate_id in sec_bnds:
var2 = sec_bnds[mate_id]
bedpe_out.write(str(converter.convert(var, var2)) + '\n')
del sec_bnds[mate_id]
else:
bnds.update({var.var_id:var})
if bnds is not None:
for bnd in bnds:
sys.stderr.write('Warning: missing secondary multiline variant at ID:' + bnd + '\n')
bedpe_out.write(str(converter.convert(bnds[bnd], None)) + '\n')
if sec_bnds is not None:
for bnd in sec_bnds:
sys.stderr.write('Warning: missing primary multiline variant at ID:' + bnd + '\n')
bedpe_out.write(str(converter.convert(None, sec_bnds[bnd])) + '\n')
# close the files
bedpe_out.close()
return
def vcfToBedpe(vcf_file, bedpe_out):
converter = VcfToBedpeConverter()
vcf = svtools.vcf.file.Vcf()
in_header = True
header = []
sample_list = []
bnds = dict()
sec_bnds = dict()
v = []
for line in vcf_file:
if in_header:
if line[0:2] == '##':
if line.split('=')[0] == '##fileformat':
line = '##fileformat=' + "BEDPE" + '\n'
if line.split('=')[0] == '##fileDate':
line = '##fileDate=' + time.strftime('%Y%m%d') + '\n'
header.append(line)
continue
elif line[0] == '#' and line[1] != '#':
sample_list = line.rstrip().split('\t')[9:]
header.append(line)
continue
else:
# print header
in_header = False
vcf.add_header(header)
if "SVTYPE" in [info.id for info in vcf.info_list]:
vcf.add_info_after(
"SVTYPE", "POS", 1, 'Integer',
'Position of the variant described in this record')
header = vcf.get_header()
bedpe_out.write(header[:header.rfind('\n')] + '\n')
final_header_line = [
'#CHROM_A', 'START_A', 'END_A', 'CHROM_B', 'START_B',
'END_B', 'ID', 'QUAL', 'STRAND_A', 'STRAND_B', 'TYPE',
'FILTER', 'NAME_A', 'REF_A', 'ALT_A', 'NAME_B', 'REF_B',
'ALT_B', 'INFO_A', 'INFO_B'
]
if len(sample_list) > 0:
bedpe_out.write('\t'.join(
final_header_line +
['FORMAT', '\t'.join(map(str, sample_list))]) + '\n')
else:
bedpe_out.write('\t'.join(final_header_line) + '\n')
v = line.rstrip().split('\t')
var = svtools.vcf.variant.Variant(v, vcf)
var.set_info("POS", var.pos)
unique_name = var.var_id
# The EVENT ID is not unique. Stick with ID column.
# if 'EVENT' in var.info:
# unique_name = var.info['EVENT']
if var.info['SVTYPE'] != 'BND':
bedpe_out.write(str(converter.convert(var)) + '\n')
else:
# Manta doesn't use the SECONDARY flag
# So, just check whether the mate ID is in bnds
# Which means that the mate has already been seen
if 'MATEID' in var.info:
mate_id = var.info['MATEID']
if mate_id in bnds:
var1 = bnds[mate_id]
bedpe_out.write(str(converter.convert(var1, var)) + '\n')
del bnds[mate_id]
else:
bnds.update({unique_name: var})
else:
bnds.update({unique_name: var})
continue
intersected_keys = bnds.viewkeys() & sec_bnds.viewkeys()
for key in intersected_keys:
bedpe_out.write(
str(converter.convert(bnds[key], sec_bnds[key])) + '\n')
del bnds[key]
del sec_bnds[key]
if bnds is not None:
for bnd in bnds:
sys.stderr.write(
'Warning: missing secondary multiline variant at ID:' + bnd +
'\n')
bedpe_out.write(str(converter.convert(bnds[bnd], None)) + '\n')
if sec_bnds is not None:
for bnd in sec_bnds:
sys.stderr.write(
'Warning: missing primary multiline variant at ID:' + bnd +
'\n')
bedpe_out.write(str(converter.convert(None, sec_bnds[bnd])) + '\n')
# close the files
bedpe_out.close()
return
