singlecellmultiomics.alleleTools package

Submodules

singlecellmultiomics.alleleTools.alleleTools module

class singlecellmultiomics.alleleTools.alleleTools.AlleleResolver(vcffile=None, chrom=None, phased=True, uglyMode=False, lazyLoad=False, select_samples=None, use_cache=False, ignore_conversions=None, verbose=False, region_start=None, region_end=None)[source]

Bases: singlecellmultiomics.utils.prefetch.Prefetcher

addAlleleInfoOneBased(chromosome, location, base, alleleName)[source]
clean_vcf_name(vcffile)[source]
fetchChromosome(vcffile, chrom, clear=False)[source]
getAllele(reads)[source]
getAllelesAt(chrom, pos, base)[source]
has_location(chrom, pos)[source]
instance(arg_update)[source]
prefetch(contig, start, end)[source]
read_cached(path, chrom)[source]

Read cache file

Parameters:
  • path (str) – path of the cache file
  • chrom (str) – contig/chromosome
write_cache(path, chrom)[source]

Write to cache file, this will make later lookups to the chromosome faster

Parameters:
  • path (str) – path of the cache file
  • chrom (str) – contig/chromosome to write cache file for (every contig has it’s own cache)
singlecellmultiomics.alleleTools.alleleTools.get_allele_dict()[source]
singlecellmultiomics.alleleTools.alleleTools.nested_set_defaultdict()[source]
singlecellmultiomics.alleleTools.alleleTools.set_defaultdict()[source]

Module contents