def filter_calls_by_sample(self, samples, reverse=False, keep_info=False):
calls = [self.get_call(sample).call for sample in samples]
if reverse:
all_samples = set([c.sample for c in self.calls])
chosen_samples = set([c.sample for c in calls])
unchosen_samples = all_samples.difference(chosen_samples)
calls = [self.get_call(sample).call for sample in unchosen_samples]
sample_indexes = {call.sample: idx for idx, call in enumerate(calls)}
alleles = set()
alleles.update([allele for call in calls if call.called for allele in call.gt_alleles])
alleles.discard('.')
int_alleles = list(map(int, alleles))
record = self.record
alt_alleles = [a for i, a in enumerate(record.ALT) if i + 1 in int_alleles]
if not alt_alleles:
alt_alleles.append(None)
info = record.INFO if keep_info else {}
record = pyvcfRecord(record.CHROM, record.POS, record.ID,
record.REF, alt_alleles, record.QUAL,
record.FILTER, info, record.FORMAT,
sample_indexes, calls)
snv = SNV(record, self.reader,
min_calls_for_pop_stats=self.min_calls_for_pop_stats)
return snv
def copy_mapping_calls(self, call_mapper):
calls = []
sample_indexes = {}
is_list = True if isinstance(call_mapper, list) else False
for index, call in enumerate(self.calls):
sample = call.sample
if is_list:
call = call_mapper[index]
else:
call = call_mapper(call)
calls.append(call)
sample_indexes[sample] = index
record = self.record
record = pyvcfRecord(record.CHROM, record.POS, record.ID,
record.REF, record.ALT, record.QUAL,
record.FILTER, record.INFO, record.FORMAT,
sample_indexes, calls)
snv = SNV(record, self.reader,
min_calls_for_pop_stats=self.min_calls_for_pop_stats)
return snv
def filter_calls_by_sample(self, samples, reverse=False, keep_info=False):
calls = [self.get_call(sample).call for sample in samples]
if reverse:
all_samples = set([c.sample for c in self.calls])
chosen_samples = set([c.sample for c in calls])
unchosen_samples = all_samples.difference(chosen_samples)
calls = [self.get_call(sample).call for sample in unchosen_samples]
sample_indexes = {call.sample: idx for idx, call in enumerate(calls)}
record = self.record
info = record.INFO if keep_info else {}
record = pyvcfRecord(record.CHROM, record.POS, record.ID, record.REF,
record.ALT, record.QUAL, record.FILTER, info,
record.FORMAT, sample_indexes, calls)
snv = SNV(record,
self.reader,
min_calls_for_pop_stats=self.min_calls_for_pop_stats)
return snv
