A fast reader for local or remote UCSC twobit sequence files.
Project description
pyTwoBit
Package for fetching sequence from twobit files from local paths or URLs.
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"
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