deeplotyper¶

deeplotyper: tools for mapping and remapping genomic ↔ transcript sequences.

Functions

`apply_alignment_gaps`(seq1, seq2, blocks1, ...)	Insert gaps so aligned blocks line up between two sequences.
`build_linear_coords`(sequence, region, ...)	Map a linear sequence to a list of RawBase objects.
`build_raw_genome_coords`(spliced, region, ...)	Generate RawBase list for a spliced genome region.
`build_raw_transcript_coords`(transcript_seq, ...)	Generate RawBase list for a transcript (always forward strand).
`find_orfs`(seq)	Identify all open reading frames (ORFs) in the given nucleotide sequence.
`get_longest_orf`(seq)	Return the longest ORF found in the sequence, as (start, end, orf_seq).
`make_aligner`([mode, match_score, ...])	Return a cached PairwiseAligner configured with custom scoring.

Classes

`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.
`SequenceCoordinateMapper`()	Maps between spliced (cDNA), transcript, and genomic sequences.

Modules

`alignment_utils`
`coordinate_utils`
`data_models`
`extras`
`mapper`
`orf_utils`
`remapper`
`vcf_haploevents`