bio-twobit 0.1.1

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data/.rubocop.yml

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+AllCops:
+  TargetRubyVersion: 2.6
+
+Style/StringLiterals:
+  Enabled: true
+  EnforcedStyle: double_quotes
+
+Style/StringLiteralsInInterpolation:
+  Enabled: true
+  EnforcedStyle: double_quotes
+
+Layout/LineLength:
+  Max: 120

data/Gemfile

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+# frozen_string_literal: true
+
+source "https://rubygems.org"
+
+# Specify your gem's dependencies in bio-twobit.gemspec
+gemspec
+
+gem "rake"
+
+gem "rake-compiler"
+
+gem "test-unit"
+
+gem "rubocop"

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2021 kojix2
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# bio-twobit
+
+[![Gem Version](https://badge.fury.io/rb/bio-twobit.svg)](https://badge.fury.io/rb/bio-twobit)
+[![test](https://github.com/ruby-on-bioc/bio-twobit/actions/workflows/ci.yml/badge.svg)](https://github.com/ruby-on-bioc/bio-twobit/actions/workflows/ci.yml)
+[![dics](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/bio-twobit)
+[![DOI](https://zenodo.org/badge/436454379.svg)](https://zenodo.org/badge/latestdoi/436454379)
+
+Ruby bindings to [lib2bit](https://github.com/dpryan79/lib2bit) / [py2bit](https://github.com/deeptools/py2bit).
+
+## Installation
+
+```sh
+gem install bio-twobit
+```
+
+## Usage
+
+Downlaod BSgenome.Hsapiens.UCSC.hg38
+
+```sh
+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
+
+```ruby
+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).
+
+```ruby
+# 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`
+
+```ruby
+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](https://opensource.org/licenses/MIT).

data/Rakefile

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+# frozen_string_literal: true
+
+require "bundler/gem_tasks"
+require "rake/testtask"
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList["test/**/*_test.rb"]
+end
+
+require "rubocop/rake_task"
+
+RuboCop::RakeTask.new
+
+require "rake/extensiontask"
+
+task build: :compile
+
+Rake::ExtensionTask.new("twobit") do |ext|
+  ext.lib_dir = "lib/bio/twobit"
+  ext.ext_dir = "ext/bio/twobit"
+end
+
+task default: %i[clobber compile test rubocop]

data/bio-twobit.gemspec

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+# frozen_string_literal: true
+
+require_relative "lib/bio/twobit/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "bio-twobit"
+  spec.version       = Bio::TwoBit::VERSION
+  spec.authors       = ["kojix2"]
+  spec.email         = ["2xijok@gmail.com"]
+
+  spec.summary       = "A ruby library for accessing 2bit files"
+  spec.description   = "This is a Ruby binding for lib2bit(https://github.com/dpryan79/lib2bit), " \
+                     "which provides high-speed access to genomic data in 2bit file format."
+  spec.homepage      = "https://github.com/ruby-on-bioc/bio-twobit"
+  spec.license       = "MIT"
+  spec.required_ruby_version = ">= 2.6.0"
+
+  spec.files = Dir.chdir(File.expand_path(__dir__)) do
+    `git ls-files -z`.split("\x0").reject do |f|
+      (f == __FILE__) || f.match(%r{\A(?:(?:test|spec|features)/|\.(?:git|travis|circleci)|appveyor)})
+    end
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{\Aexe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+  spec.extensions    = ["ext/bio/twobit/extconf.rb"]
+
+  # spec.add_dependency "example-gem", "~> 1.0"
+end