def del_vcf_constructor(self, hgvs):
if self._chr_data is None:
self.load_chr_data()
chrom = hgvs[0]
pos = int(hgvs[1]) - 1
# len=2 was a single del, len=3 was internval del
if len(hgvs) == 2:
end = int(hgvs[1])
else:
end = int(hgvs[2])
chr_bit = self._chr_data[str(chrom)]
ref = ''
for i in range(pos, end+1):
try:
nuc_chr_bit = chr_bit[i*4-4:i*4]
nuc_chr = bit_to_nuc(nuc_chr_bit)
ref += nuc_chr
except Exception as e:
self.logger.warning("Couldn't extract nucleotide from bits with HGVS %s: %s" % (repr(hgvs),e))
return None
alt = ref[0]
if chrom == 'MT':
chrom = 'M'
vcf = {"chrom": str(chrom), "position": str(pos), "ref": ref, "alt": alt}
return vcf
def ins_vcf_constructor(self, hgvs):
if self._chr_data is None:
self.load_chr_data()
chrom = hgvs[0]
pos = int(hgvs[1])
chr_bit = self._chr_data[str(chrom)]
nuc_chr_bit = chr_bit[pos * 4 - 4:pos * 4]
try:
ref = bit_to_nuc(nuc_chr_bit)
except Exception as e:
self.logger.warning(
"Couldn't extract nucleotide from bits with HGVS %s: %s" %
(repr(hgvs), e))
return None
alt = hgvs[3]
alt = ref + alt
if chrom == 'MT':
chrom = 'M'
vcf = {
"chrom": str(chrom),
"position": str(pos),
"ref": ref,
"alt": alt
}
return vcf
def del_vcf_constructor(self, hgvs):
if self._chr_data is None:
self.load_chr_data()
chrom = hgvs[0]
pos = int(hgvs[1]) - 1
# len=2 was a single del, len=3 was internval del
if len(hgvs) == 2:
end = int(hgvs[1])
else:
end = int(hgvs[2])
chr_bit = self._chr_data[str(chrom)]
ref = ''
for i in range(pos, end+1):
try:
nuc_chr_bit = chr_bit[i*4-4:i*4]
nuc_chr = bit_to_nuc(nuc_chr_bit)
ref += nuc_chr
except Exception as e:
self.logger.warning("Couldn't extract nucleotide from bits with HGVS %s: %s" % (repr(hgvs),e))
return None
alt = ref[0]
if chrom == 'MT':
chrom = 'M'
vcf = {"chrom": str(chrom), "position": str(pos), "ref": ref, "alt": alt}
return vcf
def ins_vcf_constructor(self, hgvs):
if self._chr_data is None:
print()
self.load_chr_data()
chrom = hgvs[0]
pos = int(hgvs[1])
chr_bit = self._chr_data[str(chrom)]
nuc_chr_bit = chr_bit[pos*3-3:pos*3]
ref = bit_to_nuc(nuc_chr_bit)
alt = hgvs[3]
alt = ref + alt
vcf = str(chrom) + '\t' + str(pos) + '\t' + '.' + '\t' + ref + '\t' + alt + '\t.\t.\t.\n'
return vcf
def ins_vcf_constructor(self, hgvs):
if self._chr_data is None:
print()
self.load_chr_data()
chrom = hgvs[0]
pos = int(hgvs[1])
chr_bit = self._chr_data[str(chrom)]
nuc_chr_bit = chr_bit[pos*3-3:pos*3]
ref = bit_to_nuc(nuc_chr_bit)
alt = hgvs[3]
alt = ref + alt
vcf = str(chrom) + '\t' + str(pos) + '\t' + '.' + '\t' + ref + '\t' + alt + '\t.\t.\t.\n'
return vcf
def delins_vcf_constructor(self, hgvs):
if self._chr_data is None:
print()
self.load_chr_data()
chrom = hgvs[0]
pos = int(hgvs[1])
end = int(hgvs[2])
chr_bit = self._chr_data[str(chrom)]
ref = ''
for i in range(pos, end+1):
nuc_chr_bit = chr_bit[i*3-3:i*3]
nuc_chr = bit_to_nuc(nuc_chr_bit)
ref += nuc_chr
alt = hgvs[3]
vcf = str(chrom) + '\t' + str(pos) + '\t' + '.' + '\t' + ref + '\t' + alt + '\t.\t.\t.\n'
return vcf
def delins_vcf_constructor(self, hgvs):
if self._chr_data is None:
print()
self.load_chr_data()
chrom = hgvs[0]
pos = int(hgvs[1])
end = int(hgvs[2])
chr_bit = self._chr_data[str(chrom)]
ref = ''
for i in range(pos, end+1):
nuc_chr_bit = chr_bit[i*3-3:i*3]
nuc_chr = bit_to_nuc(nuc_chr_bit)
ref += nuc_chr
alt = hgvs[3]
vcf = str(chrom) + '\t' + str(pos) + '\t' + '.' + '\t' + ref + '\t' + alt + '\t.\t.\t.\n'
return vcf
def ins_vcf_constructor(self, hgvs):
if self._chr_data is None:
self.load_chr_data()
chrom = hgvs[0]
pos = int(hgvs[1])
chr_bit = self._chr_data[str(chrom)]
nuc_chr_bit = chr_bit[pos*4-4:pos*4]
try:
ref = bit_to_nuc(nuc_chr_bit)
except Exception as e:
self.logger.warning("Couldn't extract nucleotide from bits with HGVS %s: %s" % (repr(hgvs),e))
return None
alt = hgvs[3]
alt = ref + alt
if chrom == 'MT':
chrom = 'M'
vcf = {"chrom": str(chrom), "position": str(pos), "ref": ref, "alt": alt}
return vcf
