outrigger.region module

Define locations in the genome

class outrigger.region.Region(name=None, region=None, chrom=None, start=None, stop=None, strand=None)

Bases: object

A location in the genome

Parameters:

name : str

A string of either of the two forms:

• chrom:start-stop:strand, e.g. “chr1:100-200:-“
• region:chrom:start-stop:strand, e.g. “exon:chr1:100-200:+”

Start must always be smaller than stop.

Attributes

name

Methods

overlaps(other)	Returns true if any part of other region is contained in this one
to_bed_format([name])
to_zero_based()	Convert genome coordinates to 0-based

chrom

name

overlaps(other)

Returns true if any part of other region is contained in this one

region

start

stop

strand

to_bed_format(name=None)

to_zero_based()

Convert genome coordinates to 0-based

Assumes that this event is one-based.