genomeblocks.locus

Core interval dataclasses.

Table of contents

1. Locus
   1. Properties
   2. Methods
   3. Ordering
2. Exon(Locus)
3. CDS(Exon)
4. UTR(Exon)

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Locus

@dataclass
class Locus:
    chrom: str
    start: int
    end: int
    strand: str = "."

Properties

Name	Type	Description
uid	str	Canonical "chrom:start-end(strand)" identifier.
length	int	end - start.
center	int	(start + end) // 2.

Methods

Locus.overlaps(other)       # bool — both on same chrom AND ranges intersect
Locus.distance_to(other)    # int  — |center - other.center|, NotImplemented if cross-chrom
Locus.sequence(genome, r=None)
    # Extract sequence from a {chrom: str} genome dict.
    # If r is None, returns genome[chrom][start:end].
    # Otherwise, returns a ±r bp window around center.
Locus.copy()                # new Locus with same fields

Ordering

Locus defines __lt__, __le__, __gt__, __ge__ so lists of Locus objects sort by (chrom, start).

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Exon(Locus)

@dataclass
class Exon(Locus):
    exon_number: int = 0

CDS(Exon)

Alias; same fields as Exon, used as a type marker.

UTR(Exon)

@dataclass
class UTR(Exon):
    type: str = None      # "5'" or "3'"

All three inherit Locus’s UID / overlap / distance methods, so they participate in every interval API.