MultiSampleVCF

MultiSampleVCF(self, *args, **kwargs)

NumberVariantQuery

NumberVariantQuery(self, max_num=inf, min_num=0)

Closure for variant query. Filter variants for interval if number of variants in given limits.

VariantIntervalQueryable

VariantIntervalQueryable(self, vcf, variant_intervals:List[Tuple[Iterable[kipoiseq.dataclasses.Variant], kipoiseq.dataclasses.Interval]], progress=False)

IntervalSeqBuilder

IntervalSeqBuilder(self, /, *args, **kwargs)

String builder for pyfaidx.Sequence and Interval objects.

VariantSeqExtractor

VariantSeqExtractor(self, fasta_file:str=None, reference_sequence:kipoiseq.extractors.base.BaseExtractor=None, use_strand=True)

SingleVariantVCFSeqExtractor

SingleVariantVCFSeqExtractor(self, fasta_file, vcf_file)

Fetch list of sequence in which each variant applied based on given vcf file.

SingleSeqVCFSeqExtractor

SingleSeqVCFSeqExtractor(self, fasta_file, vcf_file)

Fetch sequence in which all variant applied based on given vcf file.

variants_to_pyranges

variants_to_pyranges(variants:List[kipoiseq.dataclasses.Variant]) -> pyranges.pyranges.PyRanges

Create pyrange object given list of variant objects.

Args: variants: list of variant objects have CHROM, POS, REF, ALT properties.

BaseVariantMatcher

BaseVariantMatcher(self, vcf_file:str=None, variants:List[kipoiseq.dataclasses.Variant]=None, variant_fetcher:kipoiseq.variant_source.VariantFetcher=None, gtf_path:str=None, bed_path:str=None, pranges:pyranges.pyranges.PyRanges=None, intervals:List[kipoiseq.dataclasses.Interval]=None, interval_attrs:List[str]=None, vcf_lazy:bool=True, variant_batch_size:int=10000)

Base variant intervals matcher

SingleVariantMatcher

SingleVariantMatcher(self, *args, **kwargs)

Match and iterate variants with intervals.