def parse_vcf_record(vcf_line):
A = vcf_line.rstrip().split('\t')
if not 'SECONDARY' in A[7]:
if 'SVTYPE=BND' in A[7]:
sep, o_chr, o_pos = parse_bnd_alt_string(A[4])
if (o_chr == A[0]) and (('--:' in A[7]) != ('++' in A[7])):
neg_s = A[7].find('--:')
pos_s = A[7].find('++:')
if neg_s > 0:
neg_e = neg_s + A[7][neg_s:].find(';')
pre = A[7][:neg_s]
mid = A[7][neg_s:neg_e]
post = A[7][neg_e:]
A[7] = pre + '++:0,' + mid + post
else:
pos_e = pos_s + A[7][pos_s:].find(';')
pre = A[7][:pos_s]
mid = A[7][pos_s:pos_e]
post = A[7][pos_e:]
A[7] = pre + mid + ',--:0' + post
A[7] = 'SVTYPE=INV' + A[7][10:] + ';END=' + o_pos
A[4] = '<INV>'
vcf_line = '\t'.join(A) + '\n'
return vcf_line
def split_v(l):
'''
Split a VCF line into constituents and return a subset of values in an array
'''
A = l.rstrip().split('\t', 8)
m = to_map(A[7])
chr_l = A[0]
pos_l = int(A[1])
chr_r = A[0]
pos_r = int(A[1])
if m['SVTYPE'] == 'BND':
sep, chr_r, pos_r = parse_bnd_alt_string(A[4])
m['END'] = pos_r
pos_r = int(pos_r)
elif m['SVTYPE'] == 'INS':
pos_r = pos_l + int(m['SVLEN'])
else:
pos_r = int(m['END'])
start_l = pos_l + int(m['CIPOS'].split(',')[0])
end_l = pos_l + int(m['CIPOS'].split(',')[1])
start_r = pos_r + int(m['CIEND'].split(',')[0])
end_r = pos_r + int(m['CIEND'].split(',')[1])
strands = m['STRANDS']
return [
m['SVTYPE'], chr_l, chr_r, strands, start_l, end_l, start_r, end_r, m
]
def convert_bnd(var):
var.ref='N'
alt=var.alt
ff=alt.find("[")
newalt=""
strands=""
sep1, chrom2, breakpoint2=su.parse_bnd_alt_string(alt)
if chrom2 < var.chrom or (chrom2==var.chrom and int(breakpoint2)<int(var.pos)):
var.set_info('SECONDARY', True)
if ff==0:
strands="--:"
ff1=alt.find("[", 1)
newalt=alt[0:(ff1+1)]+'N'
elif ff>0:
strands="+-:"
newalt='N'+alt[ff::]
else:
ff=alt.find("]")
if ff==0:
strands="-+:"
ff1=alt.find("]", 1)
newalt=alt[0:(ff1+1)]+'N'
else:
strands="++:"
newalt='N'+alt[ff::]
var.alt=newalt
var.info['STRANDS']=strands+str(var.info['SU'])
def parse_vcf_record(vcf_line):
A = vcf_line.rstrip().split('\t')
if not 'SECONDARY' in A[7]:
if 'SVTYPE=BND' in A[7]:
sep, o_chr, o_pos = parse_bnd_alt_string(A[4])
if (o_chr == A[0]) and (('--:' in A[7]) != ('++' in A[7])):
neg_s = A[7].find('--:')
pos_s = A[7].find('++:')
if neg_s > 0:
neg_e = neg_s + A[7][neg_s:].find(';')
pre=A[7][:neg_s]
mid=A[7][neg_s:neg_e]
post=A[7][neg_e:]
A[7] = pre + '++:0,' + mid + post
else:
pos_e = pos_s + A[7][pos_s:].find(';')
pre=A[7][:pos_s]
mid=A[7][pos_s:pos_e]
post=A[7][pos_e:]
A[7] = pre + mid + ',--:0' + post
A[7] = 'SVTYPE=INV' + A[7][10:] + ';END=' + o_pos
A[4] = '<INV>'
vcf_line='\t'.join(A) + '\n'
return vcf_line
def split_v(l):
'''
Split a VCF line into constituents and return a subset of values in an array
'''
A = l.rstrip().split('\t', 8)
m = to_map(A[7])
chr_l = A[0]
pos_l = int(A[1])
chr_r = A[0]
pos_r = int(A[1])
if m['SVTYPE'] == 'BND':
sep, chr_r, pos_r = parse_bnd_alt_string(A[4])
m['END'] = pos_r
pos_r = int(pos_r)
else:
pos_r = int(m['END'])
start_l = pos_l + int(m['CIPOS'].split(',')[0])
end_l = pos_l + int(m['CIPOS'].split(',')[1])
start_r = pos_r + int(m['CIEND'].split(',')[0])
end_r = pos_r + int(m['CIEND'].split(',')[1])
strands = m['STRANDS']
return [m['SVTYPE'],chr_l,chr_r,strands,start_l,end_l,start_r,end_r,m]
def test_bnd_alt_string(self):
self.assertEqual(su.parse_bnd_alt_string('A[1:6['), ('[', '1', '6'))
self.assertEqual(su.parse_bnd_alt_string('A]1:6]'), (']', '1', '6'))
self.assertEqual(su.parse_bnd_alt_string(']1:6]A'), (']', '1', '6'))
self.assertEqual(su.parse_bnd_alt_string(']HLA-DQB1*06:09:01:6]A'), (']', 'HLA-DQB1*06:09:01', '6'))
with self.assertRaises(AssertionError):
su.parse_bnd_alt_string(']1:6[A')
with self.assertRaises(AssertionError):
su.parse_bnd_alt_string('1')
def test_bnd_alt_string(self):
self.assertEqual(su.parse_bnd_alt_string('A[1:6['), ('[', '1', '6'))
self.assertEqual(su.parse_bnd_alt_string('A]1:6]'), (']', '1', '6'))
self.assertEqual(su.parse_bnd_alt_string(']1:6]A'), (']', '1', '6'))
self.assertEqual(su.parse_bnd_alt_string(']HLA-DQB1*06:09:01:6]A'),
(']', 'HLA-DQB1*06:09:01', '6'))
with self.assertRaises(AssertionError):
su.parse_bnd_alt_string(']1:6[A')
with self.assertRaises(AssertionError):
su.parse_bnd_alt_string('1')
def parse_vcf(vcf_file_stream, vcf_lines, vcf_headers, add_sname=True, include_ref=False):
header = ''
samples = ''
for l in vcf_file_stream:
if l[0] == '#':
if l[1] != '#':
samples = l.rstrip().split('\t')[9:]
else:
# ignore fileDate
if l[:10] == '##fileDate':
continue
if l not in vcf_headers:
vcf_headers.append(l)
else:
A = l.rstrip().split('\t')
if not include_ref and (len(A) > 8 and 'GT' in A[8]):
has_nonref = False
for sample_field in A[9:]:
if not (sample_field.startswith('0/0') or sample_field.startswith('./.')):
has_nonref = True
break
if not has_nonref:
continue
if not 'SECONDARY' in A[7]:
if add_sname and (samples != []):
A[7] += ';' + 'SNAME=' + ','.join(samples)
l = '\t'.join(A) + '\n'
if 'SVTYPE=BND' in A[7]:
sep, o_chr, o_pos = parse_bnd_alt_string(A[4])
if (o_chr == A[0]) and (('--:' in A[7]) != ('++' in A[7])):
neg_s = A[7].find('--:')
pos_s = A[7].find('++:')
if neg_s > 0:
neg_e = neg_s + A[7][neg_s:].find(';')
pre=A[7][:neg_s]
mid=A[7][neg_s:neg_e]
post=A[7][neg_e:]
A[7] = pre + '++:0,' + mid + post
else:
pos_e = pos_s + A[7][pos_s:].find(';')
pre=A[7][:pos_s]
mid=A[7][pos_s:pos_e]
post=A[7][pos_e:]
A[7] = pre + mid + ',--:0' + post
A[7] = 'SVTYPE=INV' + A[7][10:] + ';END=' + o_pos
A[4] = '<INV>'
l = '\t'.join(A) + '\n'
vcf_lines.append(l)
return samples
def bnd_breakpoints(self, vcf_variant):
'''
Return a tuple containing calculated breakpoints and orientations for a BND variant
'''
chrom1 = vcf_variant.chrom
breakpoint1 = vcf_variant.pos
orientation1 = orientation2 = '+'
sep, chrom2, breakpoint2 = parse_bnd_alt_string(vcf_variant.alt)
breakpoint2 = int(breakpoint2)
if vcf_variant.alt.startswith(sep):
orientation1 = '-'
breakpoint1 -= 1
if sep == '[':
orientation2 = '-'
breakpoint2 -= 1
return (chrom1, breakpoint1, breakpoint1, chrom2, breakpoint2,
breakpoint2, orientation1, orientation2)
def parse_vcf(vcf_file_stream,
vcf_lines,
vcf_headers,
add_sname=True,
include_ref=False):
header = ''
samples = ''
for l in vcf_file_stream:
if l[0] == '#':
if l[1] != '#':
samples = l.rstrip().split('\t')[9:]
else:
# ignore fileDate
if l[:10] == '##fileDate':
continue
if l not in vcf_headers:
vcf_headers.append(l)
else:
A = l.rstrip().split('\t')
if not include_ref and (len(A) > 8 and 'GT' in A[8]):
has_nonref = False
for sample_field in A[9:]:
if not (sample_field.startswith('0/0')
or sample_field.startswith('./.')):
has_nonref = True
break
if not has_nonref:
continue
if not 'SECONDARY' in A[7]:
if add_sname and (samples != []):
A[7] += ';' + 'SNAME=' + ','.join(samples)
l = '\t'.join(A) + '\n'
if 'SVTYPE=BND' in A[7]:
sep, o_chr, o_pos = parse_bnd_alt_string(A[4])
if (o_chr == A[0]) and (('--:' in A[7]) != ('++' in A[7])):
neg_s = A[7].find('--:')
pos_s = A[7].find('++:')
if neg_s > 0:
neg_e = neg_s + A[7][neg_s:].find(';')
pre = A[7][:neg_s]
mid = A[7][neg_s:neg_e]
post = A[7][neg_e:]
A[7] = pre + '++:0,' + mid + post
else:
pos_e = pos_s + A[7][pos_s:].find(';')
pre = A[7][:pos_s]
mid = A[7][pos_s:pos_e]
post = A[7][pos_e:]
A[7] = pre + mid + ',--:0' + post
if ';END=' not in A[7]:
A[7] = A[7] + ';END=' + o_pos
A[7] = A[7].replace('SVTYPE=BND', 'SVTYPE=INV')
A[4] = '<INV>'
l = '\t'.join(A) + '\n'
vcf_lines.append(l)
return samples
def write_var(var, vcf_out, include_genotypes=False):
v_id = var.var_id
if var.get_info('CIPOS95') != '0,0' or var.get_info('CIEND95') != '0,0':
var.set_info('IMPRECISE', True)
else:
var.set_info('IMPRECISE', False)
if var.get_info('SVTYPE') == 'INV' and ('--:0' in var.get_info('STRANDS')
or '++:0'
in var.get_info('STRANDS')):
invtobnd(var)
if var.alt not in ['<DEL>', '<DUP>', '<INV>', '<INS>']:
var.var_id = str(v_id) + '_1'
var.set_info('EVENT', v_id)
var.set_info('MATEID', str(v_id) + '_2')
var.info.pop('END', None)
var.info.pop('SVLEN', None)
varstring = var.get_var_string(use_cached_gt_string=True)
if not include_genotypes:
varstring = '\t'.join(varstring.split('\t', 10)[:8])
vcf_out.write(varstring + '\n')
new_alt = ''
if var.alt[0] == '[':
new_alt = '[' + var.chrom + ':' + str(var.pos) + '[N'
elif var.alt[0] == ']':
new_alt = 'N[' + var.chrom + ':' + str(var.pos) + '['
elif var.alt[-1] == '[':
new_alt = ']' + var.chrom + ':' + str(var.pos) + ']N'
elif var.alt[-1] == ']':
new_alt = 'N]' + var.chrom + ':' + str(var.pos) + ']'
sep, chrom, pos = parse_bnd_alt_string(var.alt)
var.chrom = chrom
var.pos = int(pos)
var.var_id = str(v_id) + '_2'
var.set_info('MATEID', str(v_id) + '_1')
var.set_info('SECONDARY', True)
var.alt = new_alt
[tempci, temp95] = [var.get_info('CIPOS'), var.get_info('CIPOS95')]
try:
temppr = var.get_info('PRPOS')
except KeyError:
raise MissingProbabilitiesException(
'Required tag PRPOS not found.')
var.set_info('CIPOS', var.get_info('CIEND'))
var.set_info('CIEND', tempci)
var.set_info('CIPOS95', var.get_info('CIEND95'))
var.set_info('CIEND95', temp95)
try:
var.set_info('PRPOS', var.get_info('PREND'))
except KeyError:
raise MissingProbabilitiesException(
'Required tag PREND not found.')
var.set_info('PREND', temppr)
varstring = var.get_var_string(use_cached_gt_string=True)
if not include_genotypes:
varstring = '\t'.join(varstring.split('\t', 10)[:8])
vcf_out.write(varstring + '\n')
else:
varstring = var.get_var_string(use_cached_gt_string=True)
if not include_genotypes:
varstring = '\t'.join(varstring.split('\t', 10)[:8])
vcf_out.write(varstring + '\n')
def write_var(var, vcf_out, include_genotypes=False):
v_id=var.var_id
if var.get_info('CIPOS95') != '0,0' or var.get_info('CIEND95') != '0,0':
var.set_info('IMPRECISE', True)
else:
var.set_info('IMPRECISE', False)
if var.get_info('SVTYPE') == 'INV' and ('--:0' in var.get_info('STRANDS') or '++:0' in var.get_info('STRANDS')):
invtobnd(var)
if var.alt not in ['<DEL>', '<DUP>', '<INV>']:
var.var_id=str(v_id)+'_1'
var.set_info('EVENT', v_id)
var.set_info('MATEID', str(v_id)+'_2')
var.info.pop('END', None)
var.info.pop('SVLEN', None)
varstring=var.get_var_string(use_cached_gt_string=True)
if not include_genotypes:
varstring='\t'.join(varstring.split('\t', 10)[:8])
vcf_out.write(varstring+'\n')
new_alt = ''
if var.alt[0] == '[':
new_alt = '[' + var.chrom + ':' + str(var.pos) + '[N'
elif var.alt[0] == ']':
new_alt = 'N[' + var.chrom + ':' + str(var.pos) + '['
elif var.alt[-1] == '[':
new_alt = ']' + var.chrom + ':' + str(var.pos) + ']N'
elif var.alt[-1] == ']':
new_alt = 'N]' + var.chrom + ':' + str(var.pos) + ']'
sep, chrom, pos = parse_bnd_alt_string(var.alt)
var.chrom = chrom
var.pos = int(pos)
var.var_id = str(v_id)+'_2'
var.set_info('MATEID', str(v_id)+'_1')
var.set_info('SECONDARY', True)
var.alt = new_alt
[ tempci, temp95 ] = [var.get_info('CIPOS'), var.get_info('CIPOS95')]
try:
temppr = var.get_info('PRPOS')
except KeyError:
raise MissingProbabilitiesException('Required tag PRPOS not found.')
var.set_info('CIPOS', var.get_info('CIEND'))
var.set_info('CIEND', tempci)
var.set_info('CIPOS95', var.get_info('CIEND95'))
var.set_info('CIEND95', temp95 )
try:
var.set_info('PRPOS', var.get_info('PREND'))
except KeyError:
raise MissingProbabilitiesException('Required tag PREND not found.')
var.set_info('PREND', temppr )
varstring=var.get_var_string(use_cached_gt_string=True)
if not include_genotypes:
varstring='\t'.join(varstring.split('\t', 10)[:8])
vcf_out.write(varstring+'\n')
else:
varstring=var.get_var_string(use_cached_gt_string=True)
if not include_genotypes:
varstring='\t'.join(varstring.split('\t', 10)[:8])
vcf_out.write(varstring+'\n')
