bio-gggenome 0.1.0

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.
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+ lib/**/*.rb
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+ bin/*
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+ -
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+ features/**/*.feature
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+ LICENSE.txt
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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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+
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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
data/Gemfile ADDED
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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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+
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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 "rdoc", "~> 3.12"
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+ gem "bundler", ">= 1.0.0"
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+ gem "jeweler", "~> 1.8.4"
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+ gem "bio", ">= 1.4.2"
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+ gem "rdoc", "~> 3.12"
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+ end
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+ Copyright (c) 2013 Mitsuteru Nakao
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+
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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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+
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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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+
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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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+ # bio-gggenome
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+
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+ [![Build Status](https://secure.travis-ci.org/nakao/bioruby-gggenome.png)](http://travis-ci.org/nakao/bioruby-gggenome)
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+
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+ Ruby client for GGGenome the Ultrafast sequence search, http://gggenome.dbcls.jp/en/
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+
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+ Note: this software is under active development!
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+
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+ ## Installation
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+
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+ ```sh
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+ gem install bio-gggenome
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+ ```
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+
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+ ## Usage
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+
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+ ```ruby
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+ require 'bio-gggenome'
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+ db = "hg19"
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+ missmatch = 1
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+ query = "TTCATTGACAACATT"
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+ hits = Bio::GGGenome.search(db, missmatch, query)
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+
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+ hits['results'].each do |hit|
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+ hit['name'] #=> 'chr1'
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+ hit['position'] #=> 83462476
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+ hit['strand'] #=> "+"
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+ end
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+ ```
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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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+
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+ ## Project home page
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+
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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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+
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+ http://github.com/nakao/bio-gggenome
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+
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+ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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+
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+ ## Cite
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+
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+ If you use this software, please cite one of
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+
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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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+
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+ ## Biogems.info
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+
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+ This Biogem is published at [#bio-gggenome](http://biogems.info/index.html)
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+
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+ ## Copyright
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+
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+ Copyright (c) 2013 Mitsuteru Nakao. See LICENSE.txt for further details.
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+
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+ = bio-gggenome
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+
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+ {<img
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+ src="https://secure.travis-ci.org/nakao/bioruby-gggenome.png"
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+ />}[http://travis-ci.org/#!/nakao/bioruby-gggenome]
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+
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+ Full description goes here
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+
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+ Note: this software is under active development!
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+
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+ == Installation
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+
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+ gem install bio-gggenome
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+
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+ == Usage
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+
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+ == Developers
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+
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+ To use the library
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+
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+ require 'bio-gggenome'
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+
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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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+
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+ == Project home page
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+
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+ Information on the source tree, documentation, issues and how to contribute, see
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+
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+ http://github.com/nakao/bioruby-gggenome
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+
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+ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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+
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+ == Cite
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+
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+ If you use this software, please cite one of
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+
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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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+
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+ == Biogems.info
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+
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+ This Biogem is published at http://biogems.info/index.html#bio-gggenome
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+
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+ == Copyright
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+
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+ Copyright (c) 2013 Mitsuteru Nakao. See LICENSE.txt for further details.
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+
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+ # encoding: utf-8
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+
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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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+
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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://docs.rubygems.org/read/chapter/20 for more options
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+ gem.name = "bio-gggenome"
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+ gem.homepage = "http://github.com/nakao/bio-gggenome"
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+ gem.license = "MIT"
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+ gem.summary = %Q{GGGenome ruby client}
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+ gem.description = %Q{A Ruby client for GGGenome the Ultrafast sequence search}
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+ gem.email = "mitsuteru.nakao@gmail.com"
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+ gem.authors = ["Mitsuteru Nakao"]
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+ # dependencies defined in Gemfile
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+ end
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+ Jeweler::RubygemsDotOrgTasks.new
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+
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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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+
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+ task :default => :test
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+
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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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+
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+ rdoc.rdoc_dir = 'rdoc'
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+ rdoc.title = "bio-gggenome #{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
data/VERSION ADDED
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+ 0.1.0
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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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+
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+ require 'bio-gggenome/gggenome.rb'
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+
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+ require 'rubygems'
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+ require 'json'
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+ require 'uri'
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+ require 'bio'
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+
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+ module Bio
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+
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+ # Bio::GGGenome
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+ #
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+ # gggenome = Bio::GGGenome.new
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+ # hits = gggenome.search("hg19", 1, "TTCATTGACAACATT")
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+ # hits = gggenome.search("hg19", "TTCATTGACAACATT")
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+ # hits = gggenome.search("TTCATTGACAACATT")
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+ #
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+ # hits = Bio::GGGenome.search("hg19", "TTCATTGACAACATT")
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+ #
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+ class GGGenome
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+ BASE_URL = "http://gggenome.dbcls.jp"
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+
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+ def self.search(*args)
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+ new.search(args)
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+ end
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+
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+ def initialize(uri = BASE_URL)
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+ uri = URI.parse(uri) unless uri.kind_of?(URI)
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+ @pathbase = uri.path
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+ @pathbase = '/' + @pathbase unless /\A\// =~ @pathbase
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+ @pathbase = @pathbase + '/' unless /\/\z/ =~ @pathbase
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+ @http = Bio::Command.new_http(uri.host, uri.port)
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+ @header = {
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+ 'User-Agent' => "BioRuby/#{Bio::BIORUBY_VERSION_ID}"
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+ }
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+ end
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+
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+ # Search, returns a result hash.
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+ # Bio::GGGenome#search("hg19", 1, "TTCATTGACAACATT")
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+ # Bio::GGGenome#search("hg19", "TTCATTGACAACATT")
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+ # Bio::GGGenome#search(1, "TTCATTGACAACATT")
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+ # Bio::GGGenome#search("TTCATTGACAACATT")
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+ # Bio::GGGenome#search("http://gggenome.dbcls.jp/hg19/TTCATTGACAACATTGCGT.json")
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+ def search(*args)
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+ db = nil
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+ missmatch = nil
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+
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+ if args[0] =~ /^http/
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+ args[0].sub!(BASE_URL, '')
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+ args[0].sub!(/^\//,'')
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+ args[0].sub!(".json", '')
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+ args = args[0].split("/")
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+ end
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+
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+ case args.size
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+ when 1
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+ seq = args.shift
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+ when 2
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+ if args[0].to_s.strip =~ /^[0-9]+$/
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+ missmatch,seq = args
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+ else
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+ db,seq = args
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+ end
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+ when 3
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+ db,missmatch,seq = args
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+ else
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+ raise ArgumentError
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+ end
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+ query = ['', db, missmatch, seq].compact.join("/")
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+ path = query + ".json"
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+ begin
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+ response = @http.get(path, @header)
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+ rescue
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+ end
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+
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+ case response.code
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+ when "200"
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+ JSON.parse(response.body)
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+ when "302"
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+ location = response.header['Location']
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+ search(location)
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+ else
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+ nil
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+ end
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+ end
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+ end
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+
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+ end
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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 'test/unit'
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+
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+ $LOAD_PATH.unshift(File.dirname(__FILE__))
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+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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+ require 'bio-gggenome'
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+
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+ class Test::Unit::TestCase
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+ end
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+ require 'helper'
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+
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+ class TestBioGggenome < Test::Unit::TestCase
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+
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+ def test_new
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+ assert(Bio::GGGenome.new)
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+ end
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+
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+ def test_search_result_is_a_hash
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+ g = Bio::GGGenome.new
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+ hits = g.search('hg19', '1', 'TTCATTGACAACATT')
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+ assert_equal(Hash, hits.class)
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+ end
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+
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+ def test_search_arguments_3_and_2
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+ g = Bio::GGGenome.new
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+ hits = g.search('hg19', '0', 'TTCATTGACAACATT')
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+ hits1 = g.search('hg19', 'TTCATTGACAACATT')
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+ assert_equal(hits['summary'][0]['count'], hits1['summary'][0]['count'])
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+ assert_equal(hits['summary'][1]['count'], hits1['summary'][1]['count'])
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+ assert_equal(hits['summary'][0]['count_is_approx'], hits1['summary'][0]['count_is_approx'])
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+ assert_equal(hits['summary'][0]['query'], hits1['summary'][0]['query'])
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+ end
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+
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+ def test_class_method_search
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+ hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
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+ assert_equal(Hash, hits.class)
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+ end
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+
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+ def test_hits_hash_keys
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+ hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
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+ assert_equal(['database', 'error', 'results', 'summary', 'time'].sort,
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+ hits.keys.sort)
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+ end
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+
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+ def test_hits_database
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+ hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
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+ assert_equal("Human genome, GRCh37/hg19 (Feb, 2009)", hits["database"])
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+ end
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+
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+ def test_hits_error
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+ hits = Bio::GGGenome.search('hg19', '1', 'TTCATTGACAACATT')
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+ assert_equal("none", hits["error"])
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+ end
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+
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+ def test_hits_summary
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+ hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
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+ assert_equal(Array, hits["summary"].class)
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+ assert_equal(2, hits["summary"].size)
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+ assert_equal(['count', 'count_is_approx', 'query'].sort, hits["summary"][0].keys.sort)
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+ assert_equal(15, hits["summary"][0]['count'])
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+ assert_equal(false, hits["summary"][0]['count_is_approx'])
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+ assert_equal('TTCATTGACAACATT', hits["summary"][0]['query'])
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+ end
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+
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+ def test_hits_time
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+ hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
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+ assert_equal(Date.today, Date.parse(hits["time"]))
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+ end
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+
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+ def test_hits_results_size
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+ hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
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+ assert_equal(23, hits["results"].size)
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+ end
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+
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+ def test_hits_results_keys
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+ hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
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+ assert_equal(['name', 'position', 'position_end', 'snippet', 'snippet_pos', 'snippet_end', 'strand'].sort,
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+ hits["results"][0].keys.sort)
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+ end
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+
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+ def test_hits_results_0
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+ hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
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+ assert_equal("chr1", hits["results"][0]['name'])
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+ assert_equal(83462476, hits["results"][0]['position'])
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+ assert_equal(83462490, hits["results"][0]['position_end'])
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+ assert_equal("TTCTCTTCCTCCTCCTCCTCAGCCTCAACATGAAGATGATGAAAATGGAGACCTTCATCGTGATCCACTTCTAATTAATGAATAGTAAGTATATTTTCTCTTCATTGACAACATTTTTCCTCTTACTTTATTGTAAGAATACAATATACGATATATATTGCCATGCAAAATATGTGTTAATTGACTATATTATATTATTGATAGGACTTCTTGAG",
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+ hits["results"][0]['snippet'])
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+ assert_equal(83462376, hits["results"][0]['snippet_pos'])
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+ assert_equal(83462590, hits["results"][0]['snippet_end'])
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+ assert_equal("+", hits["results"][0]['strand'])
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+ end
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+
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: bio-gggenome
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+ version: !ruby/object:Gem::Version
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+ version: 0.1.0
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+ prerelease:
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+ platform: ruby
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+ authors:
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+ - Mitsuteru Nakao
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2013-08-12 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '3.12'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '3.12'
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
35
+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: 1.0.0
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+ type: :development
39
+ prerelease: false
40
+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
43
+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: 1.0.0
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+ - !ruby/object:Gem::Dependency
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+ name: jeweler
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+ requirement: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
51
+ - - ~>
52
+ - !ruby/object:Gem::Version
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+ version: 1.8.4
54
+ type: :development
55
+ prerelease: false
56
+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
58
+ requirements:
59
+ - - ~>
60
+ - !ruby/object:Gem::Version
61
+ version: 1.8.4
62
+ - !ruby/object:Gem::Dependency
63
+ name: bio
64
+ requirement: !ruby/object:Gem::Requirement
65
+ none: false
66
+ requirements:
67
+ - - ! '>='
68
+ - !ruby/object:Gem::Version
69
+ version: 1.4.2
70
+ type: :development
71
+ prerelease: false
72
+ version_requirements: !ruby/object:Gem::Requirement
73
+ none: false
74
+ requirements:
75
+ - - ! '>='
76
+ - !ruby/object:Gem::Version
77
+ version: 1.4.2
78
+ - !ruby/object:Gem::Dependency
79
+ name: rdoc
80
+ requirement: !ruby/object:Gem::Requirement
81
+ none: false
82
+ requirements:
83
+ - - ~>
84
+ - !ruby/object:Gem::Version
85
+ version: '3.12'
86
+ type: :development
87
+ prerelease: false
88
+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
90
+ requirements:
91
+ - - ~>
92
+ - !ruby/object:Gem::Version
93
+ version: '3.12'
94
+ description: A Ruby client for GGGenome the Ultrafast sequence search
95
+ email: mitsuteru.nakao@gmail.com
96
+ executables: []
97
+ extensions: []
98
+ extra_rdoc_files:
99
+ - LICENSE.txt
100
+ - README.md
101
+ - README.rdoc
102
+ files:
103
+ - .document
104
+ - .travis.yml
105
+ - Gemfile
106
+ - LICENSE.txt
107
+ - README.md
108
+ - README.rdoc
109
+ - Rakefile
110
+ - VERSION
111
+ - lib/bio-gggenome.rb
112
+ - lib/bio-gggenome/gggenome.rb
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+ - test/helper.rb
114
+ - test/test_bio-gggenome.rb
115
+ homepage: http://github.com/nakao/bio-gggenome
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+ licenses:
117
+ - MIT
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+ post_install_message:
119
+ rdoc_options: []
120
+ require_paths:
121
+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
123
+ none: false
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+ requirements:
125
+ - - ! '>='
126
+ - !ruby/object:Gem::Version
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+ version: '0'
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+ segments:
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+ - 0
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+ hash: 1277551901848741236
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
134
+ - - ! '>='
135
+ - !ruby/object:Gem::Version
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+ version: '0'
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+ requirements: []
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+ rubyforge_project:
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+ rubygems_version: 1.8.23
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+ signing_key:
141
+ specification_version: 3
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+ summary: GGGenome ruby client
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+ test_files: []