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"