alphagenome.data.genome.Junction

class alphagenome.data.genome.Junction(chromosome, start, end, strand='.', name='', info=<factory>, k=None)

Represents a splice junction.

A splice junction is a point in a pre-mRNA transcript where an intron is removed and exons are joined during RNA splicing. This class inherits from Interval and adds properties and methods specific to splice junctions.

chromosome

The chromosome name.

start

The 0-based start position of the junction.

end

The 0-based end position of the junction.

strand

The strand of the junction (‘+’ or ‘-‘).

name

An optional name for the junction.

info

An optional dictionary to store additional information.

k

An optional integer representing the number of reads supporting the splice junction.

Raises:

ValueError – If the strand is unstranded.

Attributes

Table

acceptor	Returns the acceptor site position.
donor	Returns the donor site position.
k
chromosome
start
end
info

Junction.acceptor

Returns the acceptor site position.

Junction.donor

Returns the donor site position.

Junction.k: int | None = None

Junction.name: str = ''

Junction.negative_strand

Returns True if interval is on the negative strand, False otherwise.

Junction.strand: str = '.'

Junction.width

Returns the width of the interval.

Junction.chromosome: str

Junction.start: int

Junction.end: int

Junction.info: dict[str, Any]

Methods

Table

acceptor_region([overhang])	Returns the region around the acceptor site with overhang.
dinucleotide_region()	Returns the dinucleotide regions around acceptor and donor sites.
donor_region([overhang])	Returns the region around the donor site with overhang.

Junction.acceptor_region(overhang=(250, 250))

Returns the region around the acceptor site with overhang.

Return type:

Interval

Junction.dinucleotide_region()

Returns the dinucleotide regions around acceptor and donor sites.

Return type:

tuple[Interval, Interval]

Junction.donor_region(overhang=(250, 250))

Returns the region around the donor site with overhang.

Return type:

Interval