deeplotyper 2025.10.1a0

Tools for graph based and string based mapping and remapping genomic ↔ transcript ↔ aminoacid sequences.

deeplotyper

Tools for graph based and string based mapping and remapping genomic ↔ transcript ↔ aminoacid sequences.

Installation

pip install deeplotyper

Requires

• Python ≥ 3.8
• Biopython
• pysam

Quickstart

from deeplotyper import (
    SequenceCoordinateMapper,
    HaplotypeRemapper,
    HaplotypeGroups,
    find_orfs, get_longest_orf,
    make_aligner, apply_alignment_gaps,
    build_linear_coords, build_raw_genome_coords, build_raw_transcript_coords,
    BaseCoordinateMapping, CodonCoordinateMapping,
    SequenceMappingResult, TranscriptMappingResult,
    HaplotypeEvent, NewTranscriptSequences, RawBase
)

# 1. Map a transcript to the genome
mapper = SequenceCoordinateMapper()
results = mapper.map_transcripts(
    genome_metadata={ "seq_region_accession": "chr1", "start": 100, "strand": 1 },
    full_genomic_sequence="ATGGGGTTTCCC...",
    exon_definitions_by_transcript={ "tx1": [ { "exon_number":1, "start":100, "end":102, "sequence":"ATG" }, … ] },
    transcript_sequences={ "tx1":"ATGCCC" },
    exon_orders={ "tx1":[1] },
    min_block_length=5
)

# 2. Apply SNV/indel haplotypes
hap_map = {
    ( HaplotypeEvent(pos0=2, ref_allele="A", alt_seq="G"), ): ()
}
remapper = HaplotypeRemapper("ATGAAA...", results)
mutated = remapper.apply_haplotypes(hap_map)

# 3. Group samples by haplotype from a VCF
groups = HaplotypeGroups.from_vcf("variants.vcf.gz", ref_seq="ATGAAA...", contig="1", start=0)
distinct = groups.materialize()

Package Modules

orf_utils

Functions to detect and extract open reading frames.

• find_orfs(seq: str) → List[(start,end,seq)]
• get_longest_orf(seq: str) → (start,end,orf_seq)

alignment_utils

Wrappers around Biopython’s PairwiseAligner for caching and gap insertion.

• make_aligner(...) → PairwiseAligner
• apply_alignment_gaps(seq1, seq2, blocks1, blocks2) → (gapped1, gapped2)

data_models

Typed dataclasses for coordinate‐mapping results and events.

• BaseCoordinateMapping, CodonCoordinateMapping
• SequenceMappingResult, TranscriptMappingResult
• RawBase, HaplotypeEvent, NewTranscriptSequences

coordinate_utils

Builds raw coordinate lists from sequences or exon definitions.

• build_linear_coords(sequence, region, start_pos, strand)
• build_raw_genome_coords(spliced, region, strand, start_offset, exon_order=None, exon_defs=None)
• build_raw_transcript_coords(transcript, region, start_pos)

mapper

SequenceCoordinateMapper — maps exons/transcripts to genomic coordinates at base and codon resolution, producing both gapped alignments and mapping objects.

remapper

HaplotypeRemapper — given a reference slice and transcript mappings, applies SNV/indel haplotypes to rebuild mutated genome & transcript sequences, ORFs, and all coordinate maps.

vcf_haploevents

HaplotypeGroups — read a VCF window to group samples by identical haplotype event patterns, and materialize haplotype→sample mappings.

Contributing

1. Fork the repo
2. Create a feature branch (git checkout -b feat/…)
3. Add tests under tests/ (pytest)
4. Submit a pull request

License

MIT