bio-twobit

Ruby bindings to lib2bit / py2bit.

Installation

gem install bio-twobit

Usage

Downlaod BSgenome.Hsapiens.UCSC.hg38

wget https://bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz
tar xvf BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz

Quick Start

require 'bio/twobit'

hg38 = Bio::TwoBit.open("BSgenome.Hsapiens.UCSC.hg38/inst/extdata/single_sequences.2bit")

hg38.info
# {"file_size"=>818064875,
# "nChroms"=>640,
# "sequence_length"=>3272116950,
# "hard_masked_length"=>161368694,
# "soft_masked_length"=>0}

hg38.chroms.take(5)
# [["chr1", 248956422],
# ["chr2", 242193529],
# ["chr3", 198295559],
# ["chr4", 190214555],
# ["chr5", 181538259]]

hg38.sequence("chr1", 50000, 50050)
# "AAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCC"

hg38.bases("chr1", 10000, 10100)
# {"A"=>0.34, "C"=>0.49, "T"=>0.17, "G"=>0.0}

hg38.bases("chr1", 10000, 10100, fraction: false)
# {"A"=>34, "C"=>49, "T"=>17, "G"=>0}

hg38.bases("chr1") 
# {"A"=>0.26940569141052323,
# "C"=>0.19302592242428676,
# "T"=>0.2701041550155312,
# "G"=>0.19325280952182064}

hg38.hard_masked_blocks("chr1", 0, 1000000)
# [[0, 10000], [207666, 257666], [297968, 347968], [535988, 585988]]

The 2-bit file must be closed explicitly. Alternatively, you can use a block. (If you forget to close the file, it will probably be closed by GC).

# Explicitly close the file.
tb = Bio::TwoBit.open("test/fixtures/foo.2bit")
tb.close

# You can also use blocks.
Bio::TwoBit.open("test/fixtures/foo.2bit") do |t|
  p t.info
end

If you would like to include information about soft-masked bases, you need to manually specify masked: true

tb = Bio::TwoBit.open("test/fixtures/foo.2bit")
tb.sequence("chr1", 60, 72)
# => "GTAGCTAGCTGA"

tb = Bio::TwoBit.open("test/fixtures/foo.2bit", masked: true)
tb.sequence("chr1", 60, 72)
# => "GTagctagctGA"
tb.soft_masked_blocks("chr1")
# => [[62, 70]]

Development

Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-on-bioc/bio-twobit.

License

The gem is available as open source under the terms of the MIT License.