bio-gggenome 0.1.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rdoc", "~> 3.12"
+  gem "bundler", ">= 1.0.0"
+  gem "jeweler", "~> 1.8.4"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2013 Mitsuteru Nakao
+
+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-gggenome
+
+[![Build Status](https://secure.travis-ci.org/nakao/bioruby-gggenome.png)](http://travis-ci.org/nakao/bioruby-gggenome)
+
+Ruby client for GGGenome the Ultrafast sequence search, http://gggenome.dbcls.jp/en/
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-gggenome
+```
+
+## Usage
+
+```ruby
+    require 'bio-gggenome'
+    db = "hg19"
+    missmatch = 1
+    query = "TTCATTGACAACATT"
+    hits = Bio::GGGenome.search(db, missmatch, query)
+    
+    hits['results'].each do |hit|
+      hit['name']     #=> 'chr1'
+      hit['position'] #=> 83462476
+      hit['strand']   #=> "+"
+    end
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/nakao/bio-gggenome
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#bio-gggenome](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2013 Mitsuteru Nakao. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-gggenome
+
+{<img
+src="https://secure.travis-ci.org/nakao/bioruby-gggenome.png"
+/>}[http://travis-ci.org/#!/nakao/bioruby-gggenome]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-gggenome
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-gggenome'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/nakao/bioruby-gggenome
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-gggenome
+
+== Copyright
+
+Copyright (c) 2013 Mitsuteru Nakao. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-gggenome"
+  gem.homepage = "http://github.com/nakao/bio-gggenome"
+  gem.license = "MIT"
+  gem.summary = %Q{GGGenome ruby client}
+  gem.description = %Q{A Ruby client for GGGenome the Ultrafast sequence search}
+  gem.email = "mitsuteru.nakao@gmail.com"
+  gem.authors = ["Mitsuteru Nakao"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-gggenome #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/lib/bio-gggenome.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-gggenome/gggenome.rb'
+

data/lib/bio-gggenome/gggenome.rb

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+require 'rubygems'
+require 'json'
+require 'uri'
+require 'bio'
+
+module Bio
+  
+  # Bio::GGGenome
+  #
+  # gggenome = Bio::GGGenome.new
+  # hits = gggenome.search("hg19", 1, "TTCATTGACAACATT")
+  # hits = gggenome.search("hg19", "TTCATTGACAACATT")
+  # hits = gggenome.search("TTCATTGACAACATT")
+  #
+  # hits = Bio::GGGenome.search("hg19", "TTCATTGACAACATT")
+  #
+  class GGGenome
+    BASE_URL = "http://gggenome.dbcls.jp"    
+
+    def self.search(*args)
+      new.search(args)
+    end
+        
+    def initialize(uri = BASE_URL)
+      uri = URI.parse(uri) unless uri.kind_of?(URI)
+      @pathbase = uri.path
+      @pathbase = '/' + @pathbase unless /\A\// =~ @pathbase
+      @pathbase = @pathbase + '/' unless /\/\z/ =~ @pathbase
+      @http = Bio::Command.new_http(uri.host, uri.port)
+      @header = {
+        'User-Agent' => "BioRuby/#{Bio::BIORUBY_VERSION_ID}"
+      }
+    end
+    
+    # Search, returns a result hash.
+    # Bio::GGGenome#search("hg19", 1, "TTCATTGACAACATT")
+    # Bio::GGGenome#search("hg19", "TTCATTGACAACATT")
+    # Bio::GGGenome#search(1, "TTCATTGACAACATT")
+    # Bio::GGGenome#search("TTCATTGACAACATT")
+    # Bio::GGGenome#search("http://gggenome.dbcls.jp/hg19/TTCATTGACAACATTGCGT.json")
+    def search(*args)
+      db        = nil
+      missmatch = nil
+      
+      if args[0] =~ /^http/
+        args[0].sub!(BASE_URL, '')
+        args[0].sub!(/^\//,'')
+        args[0].sub!(".json", '')
+        args = args[0].split("/")        
+      end
+      
+      case args.size
+      when 1
+        seq = args.shift
+      when 2
+        if args[0].to_s.strip =~ /^[0-9]+$/
+          missmatch,seq = args
+        else
+          db,seq = args
+        end  
+      when 3
+        db,missmatch,seq = args
+      else
+        raise ArgumentError
+      end     
+      query = ['', db, missmatch, seq].compact.join("/")
+      path =  query + ".json"
+      begin
+        response = @http.get(path, @header)
+      rescue
+      end
+
+      case response.code
+      when "200"
+        JSON.parse(response.body)
+      when "302"
+        location = response.header['Location']
+        search(location)
+      else
+        nil
+      end
+    end
+  end
+  
+end

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'bio-gggenome'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-gggenome.rb

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+require 'helper'
+
+class TestBioGggenome < Test::Unit::TestCase
+  
+  def test_new
+    assert(Bio::GGGenome.new)
+  end
+  
+  def test_search_result_is_a_hash
+    g = Bio::GGGenome.new
+    hits = g.search('hg19', '1', 'TTCATTGACAACATT')
+    assert_equal(Hash, hits.class)
+  end
+
+  def test_search_arguments_3_and_2
+    g = Bio::GGGenome.new
+    hits = g.search('hg19', '0', 'TTCATTGACAACATT')
+    hits1 = g.search('hg19',  'TTCATTGACAACATT')
+    assert_equal(hits['summary'][0]['count'],           hits1['summary'][0]['count'])
+    assert_equal(hits['summary'][1]['count'],           hits1['summary'][1]['count'])
+    assert_equal(hits['summary'][0]['count_is_approx'], hits1['summary'][0]['count_is_approx'])
+    assert_equal(hits['summary'][0]['query'],           hits1['summary'][0]['query'])
+  end
+
+  def test_class_method_search
+    hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
+    assert_equal(Hash, hits.class)
+  end
+  
+  def test_hits_hash_keys
+    hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
+    assert_equal(['database', 'error', 'results', 'summary', 'time'].sort, 
+                 hits.keys.sort)
+  end
+  
+  def test_hits_database
+    hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
+    assert_equal("Human genome, GRCh37/hg19 (Feb, 2009)", hits["database"])
+  end
+  
+  def test_hits_error
+    hits = Bio::GGGenome.search('hg19', '1', 'TTCATTGACAACATT')
+    assert_equal("none", hits["error"])
+  end
+  
+  def test_hits_summary
+    hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
+    assert_equal(Array, hits["summary"].class)
+    assert_equal(2, hits["summary"].size)
+    assert_equal(['count', 'count_is_approx', 'query'].sort, hits["summary"][0].keys.sort)
+    assert_equal(15,                hits["summary"][0]['count'])
+    assert_equal(false,             hits["summary"][0]['count_is_approx'])
+    assert_equal('TTCATTGACAACATT', hits["summary"][0]['query'])
+   end
+  
+  def test_hits_time
+    hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
+    assert_equal(Date.today, Date.parse(hits["time"]))    
+  end
+
+  def test_hits_results_size
+    hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
+    assert_equal(23, hits["results"].size)    
+  end
+
+  def test_hits_results_keys
+    hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
+    assert_equal(['name', 'position', 'position_end', 'snippet', 'snippet_pos', 'snippet_end', 'strand'].sort, 
+                 hits["results"][0].keys.sort)    
+  end
+    
+  def test_hits_results_0
+    hits = Bio::GGGenome.search('hg19', '0', 'TTCATTGACAACATT')
+    assert_equal("chr1",   hits["results"][0]['name'])    
+    assert_equal(83462476, hits["results"][0]['position'])    
+    assert_equal(83462490, hits["results"][0]['position_end'])    
+    assert_equal("TTCTCTTCCTCCTCCTCCTCAGCCTCAACATGAAGATGATGAAAATGGAGACCTTCATCGTGATCCACTTCTAATTAATGAATAGTAAGTATATTTTCTCTTCATTGACAACATTTTTCCTCTTACTTTATTGTAAGAATACAATATACGATATATATTGCCATGCAAAATATGTGTTAATTGACTATATTATATTATTGATAGGACTTCTTGAG",
+                           hits["results"][0]['snippet'])    
+    assert_equal(83462376, hits["results"][0]['snippet_pos'])    
+    assert_equal(83462590, hits["results"][0]['snippet_end'])    
+    assert_equal("+",      hits["results"][0]['strand'])    
+  end
+
+end

metadata

@@ -0,0 +1,143 @@
+--- !ruby/object:Gem::Specification
+name: bio-gggenome
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- Mitsuteru Nakao
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-08-12 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+description: A Ruby client for GGGenome the Ultrafast sequence search
+email: mitsuteru.nakao@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-gggenome.rb
+- lib/bio-gggenome/gggenome.rb
+- test/helper.rb
+- test/test_bio-gggenome.rb
+homepage: http://github.com/nakao/bio-gggenome
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 1277551901848741236
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: GGGenome ruby client
+test_files: []