deeplotyper.remapperΒΆ

Functions

get_longest_orf(seq)

Return the longest ORF found in the sequence, as (start, end, orf_seq).

Classes

Any(*args, **kwargs)

Special type indicating an unconstrained type.

CodonCoordinateMapping(codon_index, codon, ...)

Maps a codon and its amino acid across genomic and transcript coordinates.

HaplotypeEvent(pos0, ref_allele, alt_seq)

A single variant event relative to a reference haplotype.

HaplotypeRemapper(reference_genome, ...)

Given a reference genome slice and transcript mappings, produce new exon/cDNA/codon mappings under arbitrary SNV/indel haplotypes, using ORF-based translation of the longest coding region, and also return the mutated genomic sequence, coordinate maps, and a protein translation purely from the mutated genome.

NewTranscriptSequences([exon_sequences, ...])

Constructed sequences and maps after applying haplotype events.

Seq(data[, length])

Read-only sequence object (essentially a string with biological methods).