def _get_major_allele(snv):
'It returns the most frequent allele'
alleles = snv.qualifiers['alleles']
major_number_reads = None
most_freq_allele = None
for allele in alleles:
number_reads = _allele_count(allele, alleles)
if major_number_reads is None or major_number_reads < number_reads:
major_number_reads = number_reads
most_freq_allele = allele
return most_freq_allele[0]
def _create_info(self, qualifiers, alternative_alleles):
'It creates the INFO bit on the vcf'
toprint_items = []
alleles = qualifiers['alleles']
#RC allele count in genotypes, for each ALT allele, in the same order as
#listed
acounts = [] #allele_count
for allele in alternative_alleles:
acount = _allele_count(allele, alleles, group_kind='read_groups')
acounts.append(acount)
if acounts:
toprint_items.append('RC=%s' % ','.join(map(str, acounts)))
#AF allele frequency for each ALT allele in the same order as listed:
reference_allele = qualifiers['reference_allele'], INVARIANT
if reference_allele in alleles:
ref_count = _allele_count(reference_allele, alleles,
group_kind='read_groups')
else:
ref_count = 0
total_count = float(sum(acounts) + ref_count)
afreqs = [acount / total_count for acount in acounts]
if afreqs:
toprint_items.append('AF=%s' % ','.join(map(lambda x: '%.1f' % x,
afreqs)))
#MQ RMS mapping quality, e.g. MQ=52
#BQ RMS base quality at this position
for kind, strfmt in (('mapping_quality', 'MQ=%.2f'),
('quality', 'BQ=%.2f')):
qual = qualifiers[kind]
if qual is not None:
toprint_items.append(strfmt % qual)
#genotype count
#we count in how many genotypes every allele has been found.
allele_counts = self._allele_count_by_group(alleles=alleles,
reference_allele=reference_allele[0],
alternative_alleles=alternative_alleles,
read_groups=qualifiers['read_groups'],
count_reads=False)
#if some allele is missing there are 0 counts of it
n_als = max(allele_counts.keys()) + 1
genotype_counts = [(al, len(allele_counts.get(al, [])))for al in range(n_als)]
#now we print
counts = [str(count[1]) for count in genotype_counts]
toprint_items.append('GC=%s' % (','.join(counts)))
#genotype polymorphism
#1 - (number_groups_for_the_allele_with_more_groups / number_groups)
number_of_groups = sum([count[1] for count in genotype_counts])
genotype_polymorphism = 1 - genotype_counts[0][1] / float(number_of_groups)
toprint_items.append('GP=%.2f' % genotype_polymorphism)
#cap enzymes
if 'cap_enzymes' in qualifiers and qualifiers['cap_enzymes']:
to_print = 'EZ=%s' % ','.join(qualifiers['cap_enzymes'])
toprint_items.append(to_print)
if toprint_items:
return ';'.join(toprint_items)
else:
return '.'