deeplotyper.mapper

Functions

apply_alignment_gaps(seq1, seq2, blocks1, ...)	Insert gaps so aligned blocks line up between two sequences.
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).
make_aligner([mode, match_score, ...])	Return a cached PairwiseAligner configured with custom scoring.

Classes

BaseCoordinateMapping(global_position, ...)	Maps a single base between global, genomic, and transcript coordinates.
CodonCoordinateMapping(codon_index, codon, ...)	Maps a codon and its amino acid across genomic and transcript coordinates.
ExonDef	Definition of an exon segment.
MappingEntry	Mapping between transcript and genomic indices.
RawBase(region, position, base)	A raw base in a given region before any alignment or mapping.
Seq(data[, length])	Read-only sequence object (essentially a string with biological methods).
SequenceCoordinateMapper()	Maps between spliced (cDNA), transcript, and genomic sequences.
SequenceMappingResult([base_mappings, ...])	Result of mapping an entire transcript against the genome at base resolution.
TranscriptMappingResult([...])	Comprehensive mapping results for a single transcript.
defaultdict	defaultdict(default_factory=None, /, [...]) --> dict with default factory