pytwobit 0.3.0

A fast reader for local or remote UCSC twobit sequence files.

pyTwobit

Package for fetching sequence from twobit files from local paths or URLs.

Installing

pip install pyTwobit

Usage

To fetch sequence for a genomic region create a TwoBit object with either a local file path or url. Sequence is fetched with the fetch function which takes chromosome name, start, and end coordinates. The UCSC coordinate convention is used (0 start, half-open).

Local file

from pytwobit import TwoBit

twobit = TwoBit('test.2bit')
seq = twobit.fetch("chr1", 50, 57)  # -> "CTATCTA"

Remote file

from pytwobit import TwoBit

twobit = TwoBit("https://igv.org/genomes/data/hg38/hg38.2bit")
seq = twobit.fetch("chr1", 120565294, 120565335)  # -> "TATGAACTTTTGTTCGTTGGTgctcagtcctagaccctttt"