bedspec

An HTS-specs compliant BED toolkit.

Installation

The package can be installed with pip:

pip install bedspec

Quickstart

Writing

from bedspec import BedWriter, Bed3

bed = Bed3("chr1", start=2, end=8)

with BedWriter(open("test.bed", "w")) as writer:
    writer.write(bed)

Reading

from bedspec import BedReader, Bed3

with BedReader[Bed3](open("test.bed")) as reader:
    for bed in reader:
        print(bed)

Bed3(contig="chr1", start=2, start=8)

BED Types

This package provides pre-defined classes for the following BED formats:

from bedspec import Bed2
from bedspec import Bed3
from bedspec import Bed4
from bedspec import Bed5
from bedspec import Bed6
from bedspec import BedPE

Custom BED Types

To create a custom BED record, inherit from the relevent BED-type:

For example, to create a custom BED3+1 class:

from dataclasses import dataclass

from bedspec import SimpleBed

@dataclass
class MyCustomBed(SimpleBed):
    contig: str
    start: int
    end: int
    my_custom_field: float

Development and Testing

See the contributing guide for more information.