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.

negative_strand

True if the junction is on the negative (‘-’) strand.

acceptor

Position of the splice acceptor site.

donor

Position of the splice donor site.

Raises:

ValueError – If the strand is unstranded.

Methods

acceptor_region([overhang])	Returns the region around the acceptor site with overhang.
as_unstranded()	Returns an unstranded copy of the interval.
binary_mask(intervals[, bin_size])	Boolean mask True if any interval overlaps the bin: coverage > 0.
binary_mask_stranded(intervals[, bin_size])	Stranded boolean mask that is True where any interval overlaps the bin.
boundary_shift([start_offset, end_offset, ...])	Extends or shrinks the interval by adjusting the positions with padding.
center([use_strand])	Computes the center of the interval.
contains(interval)	Checks if this interval completely contains another interval.
copy()	Returns a deep copy of the interval.
coverage(intervals, *[, bin_size])	Computes coverage track from sequence of intervals overlapping interval.
coverage_stranded(intervals, *[, bin_size])	Computes a coverage track from intervals overlapping this interval.
dinucleotide_region()	Returns the dinucleotide regions around acceptor and donor sites.
donor_region([overhang])	Returns the region around the donor site with overhang.
from_interval_dict(interval)	Creates an Interval from a dictionary.
from_str(string)	Creates an Interval from a string (e.g., 'chr1:100-200:+').
intersect(interval)	Returns the intersection of this interval with another interval.
overlap_ranges(intervals)	Returns overlapping ranges from intervals overlapping this interval.
overlaps(interval)	Checks if this interval overlaps with another interval.
pad(start_pad, end_pad, *[, use_strand])	Pads the interval by adding the specified padding to the start and end.
resize(width[, use_strand])	Resizes the interval to a new width, centered around the original center.
shift(offset[, use_strand])	Shifts the interval by the given offset.
swap_strand()	Swaps the strand of the interval.
to_interval_dict()	Converts the interval to a dictionary.
truncate([reference_length])	Truncates the interval to fit within the valid reference range.
within_reference([reference_length])	Checks if the interval is within the valid reference range.