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)[source]

Bases: object

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]
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)

Module contents