fusion-function 0.2.1__py3-none-any.whl

fusion_function/ensembl.py

@@ -0,0 +1,149 @@
+from __future__ import annotations
+
+from pathlib import Path
+from typing import TYPE_CHECKING, Literal, NotRequired, TypedDict
+
+from .reference import get_reference
+
+if TYPE_CHECKING:
+    from .data import ReferenceReader
+
+
+Strand = Literal[-1, 1]
+
+
+class ProteinFeatureAnnotation(TypedDict):
+    name: str | None
+    entry_type: str | None
+    interpro_id: str | None
+
+
+class TranscriptExon(TypedDict):
+    exon_number: int
+    chromosome: str | None
+    genomic_start: int
+    genomic_end: int
+    premrna_start: int
+    premrna_end: int
+
+
+class CDSBlock(TypedDict):
+    chromosome: str | None
+    genomic_start: int
+    genomic_end: int
+    premrna_start: int
+    premrna_end: int
+    strand: Strand
+    assembly_name: str | None
+    cds_start: int
+    cds_end: int
+
+
+class GenomicSegment(TypedDict):
+    chromosome: str | None
+    start: int
+    end: int
+    strand: Strand
+    assembly_name: str | None
+
+
+class FeatureEvidence(TypedDict):
+    code: str
+    source: NotRequired[str]
+    id: NotRequired[str]
+
+
+class ProteinFeature(TypedDict):
+    feature_id: str | None
+    source: str | None
+    interpro_id: str | None
+    start: int
+    end: int
+    cds_start: int
+    cds_end: int
+    chromosome: str | None
+    genomic_start: int | None
+    genomic_end: int | None
+    strand: Strand | None
+    assembly_name: str | None
+    description: str | None
+    panther_subfamily_id: str | None
+    panther_subfamily_description: str | None
+    interpro_name: NotRequired[str | None]
+    interpro_entry_type: NotRequired[str | None]
+    genomic_segments: NotRequired[list[GenomicSegment]]
+    feature_type: NotRequired[str]
+    uniprot_accession: NotRequired[str]
+    uniprot_isoform: NotRequired[str]
+    evidence: NotRequired[list[FeatureEvidence]]
+
+
+def feature_identity(feature: ProteinFeature) -> tuple[object, ...]:
+    """Collapse only identical feature intervals, never overlapping boundaries.
+
+    Integrated signatures may share an InterPro ID and exact interval. Features
+    without one need their source, accession and description to distinguish, for
+    example, different ligand-binding annotations at the same residue.
+    """
+    identity = (
+        (feature["interpro_id"],)
+        if feature["interpro_id"]
+        else (
+            feature["source"],
+            feature["feature_id"],
+            feature["description"],
+            feature.get("uniprot_accession"),
+            feature.get("uniprot_isoform"),
+        )
+    )
+    return (
+        *identity,
+        feature["start"],
+        feature["end"],
+        feature.get("feature_type") or feature.get("interpro_entry_type"),
+    )
+
+
+class ReferenceSpliceSite(TypedDict):
+    type: Literal["donor", "acceptor"]
+    exon_number: int
+    genomic_position: int
+    premrna_position: int
+    disruption_start: int
+    disruption_end: int
+
+
+class TranscriptProteinFeatureResult(TypedDict):
+    translation_id: str | None
+    protein_length: int | None
+    chromosome: str | None
+    strand: Strand
+    transcript_genomic_start: int
+    transcript_genomic_end: int
+    premrna_length: int
+    premrna_sequence: NotRequired[str]
+    transcript_exons: list[TranscriptExon]
+    cds_blocks: list[CDSBlock]
+    cds_start_phase: NotRequired[int]
+    protein_features: list[ProteinFeature]
+    splice_sites: list[ReferenceSpliceSite]
+    assembly_name: NotRequired[str | None]
+
+
+class EnsemblError(TypedDict):
+    error: str
+
+
+ProteinFeatureResponse = TranscriptProteinFeatureResult | EnsemblError
+
+
+def get_protein_domains(
+    transcript_id: str,
+    *,
+    reference: ReferenceReader | None = None,
+    database: str | Path | None = None,
+    release: int | None = None,
+) -> ProteinFeatureResponse:
+    """Read prepared transcript structure, sequence and protein features locally."""
+    reader = get_reference(reference=reference, database=database, release=release)
+    return reader.get_transcript(transcript_id)