bio-faidx 0.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.document +5 -0
- data/.travis.yml +13 -0
- data/Gemfile +15 -0
- data/LICENSE.txt +20 -0
- data/README.md +47 -0
- data/README.rdoc +48 -0
- data/Rakefile +51 -0
- data/VERSION +1 -0
- data/lib/bio-faidx.rb +12 -0
- data/lib/bio-faidx/faidx.rb +174 -0
- data/test/helper.rb +34 -0
- data/test/test_bio-faidx.rb +7 -0
- metadata +143 -0
checksums.yaml
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---
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SHA1:
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metadata.gz: 1c78d17dec354ee49f73fcf3b9ad112b4f2eb29d
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data.tar.gz: 131d2aceda2d2be6df0686fb525b9883c97643ae
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SHA512:
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metadata.gz: 92a83e738d87455b096a3e537878ea2fb864211cf5d19730145fe665c1abf88d9576f42bd9328122e430069cbed5699240c4e04f9c35431a0693058953a6d63e
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data.tar.gz: c1bbf2b36f518fab44ee32c6a80974e59352a8cc96902dd4678c443cb90efd32143e9e40af1a9ee5769c35589cb7a45731e2ed90d95dfcc6332155d320d1de66
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data/.document
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data/.travis.yml
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language: ruby
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rvm:
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- 1.9.2
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- 1.9.3
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- jruby-19mode # JRuby in 1.9 mode
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# - rbx-19mode
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# - 1.8.7
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# - jruby-18mode # JRuby in 1.8 mode
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# - rbx-18mode
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# uncomment this line if your project needs to run something other than `rake`:
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# script: bundle exec rspec spec
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data/Gemfile
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source "http://rubygems.org"
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# Add dependencies required to use your gem here.
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# Example:
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# gem "activesupport", ">= 2.3.5"
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# Add dependencies to develop your gem here.
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# Include everything needed to run rake, tests, features, etc.
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group :development do
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gem "shoulda", ">= 0"
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gem "rdoc", "~> 3.12"
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gem "simplecov", ">= 0"
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gem "jeweler", "~> 2.0.1", :git => "https://github.com/technicalpickles/jeweler.git"
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gem "bundler", ">= 1.0.21"
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gem "bio", ">= 1.4.2"
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end
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data/LICENSE.txt
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Copyright (c) 2014 homonecloco
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# bio-faidx
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[](http://travis-ci.org/homonecloco/bioruby-faidx)
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API to work with the fai format produced to samtools. Useful if you don't want to rely on all the samtools component.
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Can query sequences from the fasta file. At the minute, it uses bio-samtools, but the idea is to make this self-sufficient.
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## Installation
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```sh
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gem install bio-faidx
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```
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## Usage
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```ruby
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require 'bio-faidx'
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```
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The API doc is online. For more code examples see the test files in
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the source tree.
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## Project home page
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Information on the source tree, documentation, examples, issues and
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how to contribute, see
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http://github.com/homonecloco/bioruby-faidx
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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## Cite
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If you use this software, please cite one of
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* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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## Biogems.info
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This Biogem is published at (http://biogems.info/index.html#bio-faidx)
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## Copyright
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Copyright (c) 2014 homonecloco. See LICENSE.txt for further details.
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data/README.rdoc
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= bio-faidx
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{<img
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src="https://secure.travis-ci.org/homonecloco/bioruby-faidx.png"
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/>}[http://travis-ci.org/#!/homonecloco/bioruby-faidx]
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Full description goes here
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Note: this software is under active development!
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== Installation
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gem install bio-faidx
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== Usage
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== Developers
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To use the library
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require 'bio-faidx'
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The API doc is online. For more code examples see also the test files in
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the source tree.
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== Project home page
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Information on the source tree, documentation, issues and how to contribute, see
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http://github.com/homonecloco/bioruby-faidx
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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== Cite
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If you use this software, please cite one of
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* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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== Biogems.info
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This Biogem is published at http://biogems.info/index.html#bio-faidx
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== Copyright
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Copyright (c) 2014 homonecloco. See LICENSE.txt for further details.
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data/Rakefile
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# encoding: utf-8
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require 'rubygems'
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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end
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require 'rake'
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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# gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
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gem.name = "bio-faidx"
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gem.homepage = "http://github.com/homonecloco/bioruby-faidx"
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gem.license = "MIT"
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gem.summary = %Q{Tools to work with fasta files, indexed with samtools}
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gem.description = %Q{ools to work with fasta files, indexed with samtools. The initial releases depend on bio-samtools, but that will change}
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gem.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"
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gem.authors = ["homonecloco"]
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# dependencies defined in Gemfile
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end
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Jeweler::RubygemsDotOrgTasks.new
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require 'rake/testtask'
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Rake::TestTask.new(:test) do |test|
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test.libs << 'lib' << 'test'
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test.pattern = 'test/**/test_*.rb'
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test.verbose = true
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end
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desc "Code coverage detail"
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task :simplecov do
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ENV['COVERAGE'] = "true"
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Rake::Task['test'].execute
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end
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task :default => :test
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require 'rdoc/task'
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Rake::RDocTask.new do |rdoc|
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version = File.exist?('VERSION') ? File.read('VERSION') : ""
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "bio-faidx #{version}"
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rdoc.rdoc_files.include('README*')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/VERSION
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0.0.1
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data/lib/bio-faidx.rb
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# Please require your code below, respecting the naming conventions in the
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# bioruby directory tree.
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#
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# For example, say you have a plugin named bio-plugin, the only uncommented
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# line in this file would be
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#
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# require 'bio/bio-plugin/plugin'
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#
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# In this file only require other files. Avoid other source code.
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require 'bio-faidx/faidx.rb'
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require 'csv'
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require 'bio-samtools'
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class Bio::DB::Faidx
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class Entry
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attr_accessor :name, :length, :offset, :linebases, :linewidth
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end
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def initialize(opts)
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@cache = false
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@cache = opts[:cache] if opts[:cache]
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@filename = opts[:filename]
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@inited = false
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end
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def init_cache
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@inited = true
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@entries = Hash.new
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@entries_order = Array.new
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read_entries do |e|
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@entries[e.name] = e
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@entries_order << e.name
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end
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end
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def entries
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init_cache unless @inited
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@entries
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end
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def [](entry)
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init_cache unless @inited
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@entries[entry]
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end
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def entries_order
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init_cache unless @inited
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return @entries_order
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end
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def read_entries
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CSV.foreach(@filename, :col_sep => "\t", :skip_lines=>/^#/, :skip_blanks=>true) do |row|
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fasta_entry = Bio::DB::Faidx::Entry.new
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[:name, :length, :offset, :linebases, :linewidth].each_with_index do |sym, i|
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answer = row[i]
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answer = answer.to_i if [:length, :offset, :linebases, :linewidth].include?(sym)
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fasta_entry.send("#{sym}=".to_sym, answer)
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yield fasta_entry
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end
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end
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def each_entry
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unless @cache
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read_entries { |e| yield e }
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else
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entries_order.each { |e| yield @entries[e] }
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end
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end
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end
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class Bio::DB::Fasta::Region
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def overlaps (other)
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return false if other.entry != @entry
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return true if other.start >= @start and other.start <= @end
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return true if other.end >= @start and other.end <= @end
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return false
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end
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def subset (other)
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return false if other.entry != @entry
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return true if other.start >= @start and other.end <= @end
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end
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def joinRegion (other)
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return nil unless self.overlaps(other)
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out = self.clone
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out.start = other.start if other.start < out.start
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out.end = other.end if other.end > out.end
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return out
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end
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def overlap_in_set(set)
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overlap_set = Set.new
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set.each do |e|
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overlap_set << e if self.overlaps(e)
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end
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overlap_set
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end
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end
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#class Faidx
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class Entry
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attr_accessor :name, :length, :offset, :linebases, :linewidth
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end
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def initialize(opts)
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@cache = false
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@cache = opts[:cache] if opts[:cache]
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@filename = opts[:filename]
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@inited = false
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end
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def init_cache
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@inited = true
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@entries = Hash.new
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@entries_order = Array.new
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read_entries do |e|
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@entries[e.name] = e
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@entries_order << e.name
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end
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end
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def entries
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init_cache unless @inited
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@entries
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end
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def entries_order
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init_cache unless @inited
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return @entries_order
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end
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def read_entries
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CSV.foreach(@filename, :col_sep => "\t", :skip_lines=>/^#/, :skip_blanks=>true) do |row|
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fasta_entry = Bio::DB::Faidx::Entry.new
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[:name, :length, :offset, :linebases, :linewidth].each_with_index do |sym, i|
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answer = row[i]
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answer = answer.to_i if [:length, :offset, :linebases, :linewidth].include?(sym)
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fasta_entry.send("#{sym}=".to_sym, answer)
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yield fasta_entry
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end
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end
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def each_entry
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unless @cache
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read_entries { |e| yield e }
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else
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entries_order.each { |e| yield @entries[e] }
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end
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end
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end
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end
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class Bio::DB::Fasta::Region
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|
+
def overlaps (other)
|
148
|
+
return false if other.entry != @entry
|
149
|
+
return true if other.start >= @start and other.start <= @end
|
150
|
+
return true if other.end >= @start and other.end <= @end
|
151
|
+
return false
|
152
|
+
end
|
153
|
+
|
154
|
+
def subset (other)
|
155
|
+
return false if other.entry != @entry
|
156
|
+
return true if other.start >= @start and other.end <= @end
|
157
|
+
end
|
158
|
+
|
159
|
+
def joinRegion (other)
|
160
|
+
return nil unless self.overlaps(other)
|
161
|
+
out = self.clone
|
162
|
+
out.start = other.start if other.start < out.start
|
163
|
+
out.end = other.end if other.end > out.end
|
164
|
+
return out
|
165
|
+
end
|
166
|
+
|
167
|
+
def overlap_in_set(set)
|
168
|
+
overlap_set = Set.new
|
169
|
+
set.each do |e|
|
170
|
+
overlap_set << e if self.overlaps(e)
|
171
|
+
end
|
172
|
+
overlap_set
|
173
|
+
end
|
174
|
+
end
|
data/test/helper.rb
ADDED
@@ -0,0 +1,34 @@
|
|
1
|
+
require 'simplecov'
|
2
|
+
|
3
|
+
module SimpleCov::Configuration
|
4
|
+
def clean_filters
|
5
|
+
@filters = []
|
6
|
+
end
|
7
|
+
end
|
8
|
+
|
9
|
+
SimpleCov.configure do
|
10
|
+
clean_filters
|
11
|
+
load_adapter 'test_frameworks'
|
12
|
+
end
|
13
|
+
|
14
|
+
ENV["COVERAGE"] && SimpleCov.start do
|
15
|
+
add_filter "/.rvm/"
|
16
|
+
end
|
17
|
+
require 'rubygems'
|
18
|
+
require 'bundler'
|
19
|
+
begin
|
20
|
+
Bundler.setup(:default, :development)
|
21
|
+
rescue Bundler::BundlerError => e
|
22
|
+
$stderr.puts e.message
|
23
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
24
|
+
exit e.status_code
|
25
|
+
end
|
26
|
+
require 'test/unit'
|
27
|
+
require 'shoulda'
|
28
|
+
|
29
|
+
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
30
|
+
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
31
|
+
require 'bio-faidx'
|
32
|
+
|
33
|
+
class Test::Unit::TestCase
|
34
|
+
end
|
metadata
ADDED
@@ -0,0 +1,143 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: bio-faidx
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.1
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- homonecloco
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2014-10-07 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: shoulda
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - ">="
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '0'
|
20
|
+
type: :development
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - ">="
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '0'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: rdoc
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - "~>"
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '3.12'
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - "~>"
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '3.12'
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: simplecov
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - ">="
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '0'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - ">="
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '0'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: jeweler
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - "~>"
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: 2.0.1
|
62
|
+
type: :development
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - "~>"
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: 2.0.1
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: bundler
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - ">="
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: 1.0.21
|
76
|
+
type: :development
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - ">="
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: 1.0.21
|
83
|
+
- !ruby/object:Gem::Dependency
|
84
|
+
name: bio
|
85
|
+
requirement: !ruby/object:Gem::Requirement
|
86
|
+
requirements:
|
87
|
+
- - ">="
|
88
|
+
- !ruby/object:Gem::Version
|
89
|
+
version: 1.4.2
|
90
|
+
type: :development
|
91
|
+
prerelease: false
|
92
|
+
version_requirements: !ruby/object:Gem::Requirement
|
93
|
+
requirements:
|
94
|
+
- - ">="
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: 1.4.2
|
97
|
+
description: ools to work with fasta files, indexed with samtools. The initial releases
|
98
|
+
depend on bio-samtools, but that will change
|
99
|
+
email: ricardo.ramirez-gonzalez@tgac.ac.uk
|
100
|
+
executables: []
|
101
|
+
extensions: []
|
102
|
+
extra_rdoc_files:
|
103
|
+
- LICENSE.txt
|
104
|
+
- README.md
|
105
|
+
- README.rdoc
|
106
|
+
files:
|
107
|
+
- ".document"
|
108
|
+
- ".travis.yml"
|
109
|
+
- Gemfile
|
110
|
+
- LICENSE.txt
|
111
|
+
- README.md
|
112
|
+
- README.rdoc
|
113
|
+
- Rakefile
|
114
|
+
- VERSION
|
115
|
+
- lib/bio-faidx.rb
|
116
|
+
- lib/bio-faidx/faidx.rb
|
117
|
+
- test/helper.rb
|
118
|
+
- test/test_bio-faidx.rb
|
119
|
+
homepage: http://github.com/homonecloco/bioruby-faidx
|
120
|
+
licenses:
|
121
|
+
- MIT
|
122
|
+
metadata: {}
|
123
|
+
post_install_message:
|
124
|
+
rdoc_options: []
|
125
|
+
require_paths:
|
126
|
+
- lib
|
127
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
128
|
+
requirements:
|
129
|
+
- - ">="
|
130
|
+
- !ruby/object:Gem::Version
|
131
|
+
version: '0'
|
132
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
133
|
+
requirements:
|
134
|
+
- - ">="
|
135
|
+
- !ruby/object:Gem::Version
|
136
|
+
version: '0'
|
137
|
+
requirements: []
|
138
|
+
rubyforge_project:
|
139
|
+
rubygems_version: 2.2.1
|
140
|
+
signing_key:
|
141
|
+
specification_version: 4
|
142
|
+
summary: Tools to work with fasta files, indexed with samtools
|
143
|
+
test_files: []
|