gtgt.Bed

class gtgt.Bed(chrom: str | None = None, chromStart: int | None = None, chromEnd: int | None = None, name: str = '.', score: int = 0, strand: str = '.', thickStart: int | None = None, thickEnd: int | None = None, itemRgb: tuple[int, ...] = (0, 0, 0), blockCount: int | None = None, blockSizes: list[int] | None = None, blockStarts: list[int] | None = None, **ignored: Any)

__init__(chrom: str | None = None, chromStart: int | None = None, chromEnd: int | None = None, name: str = '.', score: int = 0, strand: str = '.', thickStart: int | None = None, thickEnd: int | None = None, itemRgb: tuple[int, ...] = (0, 0, 0), blockCount: int | None = None, blockSizes: list[int] | None = None, blockStarts: list[int] | None = None, **ignored: Any) → None

Methods

__init__([chrom, chromStart, chromEnd, ...])
blocks()	Iterate over all blocks in the Bed record
compare(other)	Compare the size of Bed objects
compare_basepair(other)	Compare the size of Bed objects, return a string showing remainting basepairs
from_bedfile(line)	Create a BED record from a line from a Bed file
from_blocks(chrom, blocks)	Create a Bed record from multiple Ranges
intersect(other)	Update record to only contain features that overlap other
overlap(other)	All blocks from self that (partially) overlap blocks from other
subtract(other)	Subtract the blocks in other from blocks in self
update(ranges)	Update a Bed object with a list of ranges
validate()	Validate the internal constistence of the Bed record

Attributes

size	The size of a Bed record is the sum of its blocks