bio-twobit 0.1.1

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data/lib/bio/twobit.rb ADDED
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+ # frozen_string_literal: true
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+
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+ require_relative "twobit/version"
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+ require_relative "twobit/twobit"
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+
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+ module Bio
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+ class TwoBit
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+ class << self
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+ alias open new
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+ end
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+
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+ def initialize(fname, masked: false)
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+ mskd = masked ? 1 : 0
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+ initialize_raw(fname, mskd)
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+ if block_given?
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+ begin
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+ yield self
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+ ensure
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+ close
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+ end
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+ end
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+ end
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+
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+ def sequence(chrom, start = 0, stop = 0)
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+ sequence_raw(chrom, start, stop)
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+ end
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+
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+ def bases(chrom, start = 0, stop = 0, fraction: true)
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+ bases_raw(chrom, start, stop, fraction ? 1 : 0)
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+ end
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+
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+ def hard_masked_blocks(chrom, start = 0, stop = 0)
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+ hard_masked_blocks_raw(chrom, start, stop)
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+ end
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+
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+ def soft_masked_blocks(chrom, start = 0, stop = 0)
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+ soft_masked_blocks_raw(chrom, start, stop)
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+ end
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+ end
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: bio-twobit
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+ version: !ruby/object:Gem::Version
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+ version: 0.1.1
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+ platform: ruby
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+ authors:
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+ - kojix2
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+ autorequire:
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+ bindir: exe
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+ cert_chain: []
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+ date: 2021-12-18 00:00:00.000000000 Z
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+ dependencies: []
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+ description: This is a Ruby binding for lib2bit(https://github.com/dpryan79/lib2bit),
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+ which provides high-speed access to genomic data in 2bit file format.
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+ email:
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+ - 2xijok@gmail.com
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+ executables: []
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+ extensions:
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+ - ext/bio/twobit/extconf.rb
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+ extra_rdoc_files: []
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+ files:
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+ - ".rubocop.yml"
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+ - Gemfile
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+ - LICENSE.txt
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+ - README.md
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+ - Rakefile
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+ - bio-twobit.gemspec
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+ - ext/bio/twobit/2bit.c
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+ - ext/bio/twobit/2bit.h
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+ - ext/bio/twobit/LICENSE
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+ - ext/bio/twobit/extconf.rb
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+ - ext/bio/twobit/twobit.c
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+ - ext/bio/twobit/twobit.h
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+ - lib/bio/twobit.rb
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+ - lib/bio/twobit/version.rb
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+ homepage: https://github.com/ruby-on-bioc/bio-twobit
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+ licenses:
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+ - MIT
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+ metadata: {}
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+ post_install_message:
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+ rdoc_options: []
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+ require_paths:
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+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 2.6.0
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ requirements: []
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+ rubygems_version: 3.2.22
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+ signing_key:
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+ specification_version: 4
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+ summary: A ruby library for accessing 2bit files
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+ test_files: []