Interval

class alphagenome.data.genome.Interval(chromosome, start, end, strand='.', name='', info=<factory>)

Represents a genomic interval.

A genomic interval is a region on a chromosome defined by a start and end position. This class provides methods for manipulating and comparing intervals, and for calculating coverage and overlap.

chromosome

The chromosome name (e.g., ‘chr1’, ‘1’).

start

The 0-based start position.

end

The 0-based end position (must be greater than or equal to start).

strand

The strand of the interval (‘+’, ‘-’, or ‘.’). Defaults to ‘.’ (unstranded).

name

An optional name for the interval.

info

An optional dictionary to store additional information.

negative_strand

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

width

The width of the interval (end - start).

Methods

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.
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.