CodonUsage 0.0.1

checksums.yaml

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+SHA1:
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+  data.tar.gz: 290248d2dfb0913d68195e3bebc571400e650a75
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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/CodonUsage.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'CodonUsage/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "CodonUsage"
+  spec.version       = CodonUsage::VERSION
+  spec.authors       = ["proxhotdog"]
+  spec.email         = ["hotdogcheng@gmail.com"]
+  spec.summary       = %q{A ruby gem that parses codon table from http://www.kazusa.or.jp/codon}
+  spec.description   = %q{A ruby gem that parses codon table from http://www.kazusa.or.jp/codon and turn it to hash or JSON}
+  spec.homepage      = ""
+  spec.license       = "GPLv3"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.5"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "rspec", "~> 2.14"
+end

data/Gemfile

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+source 'https://rubygems.org'
+gem "CodonTable", :git => "git://github.com/proxhotdog/codonTable.git"
+# Specify your gem's dependencies in CodonUsage.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2014 proxhotdog
+
+MIT License
+
+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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+# CodonUsage
+A ruby gem that parse Codon Usage table provided by: http://www.kazusa.or.jp/codon/
+
+
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'CodonUsage'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install CodonUsage
+
+## Usage
+    require "CodonUsage"
+    foo = CodonUsage::KazusaDB.new(aa = "1", species = "9606")
+    p foo.getURL
+    p foo.getHash
+    p foo.toJSON
+
+
+for aa, it is the codon translation table, default = "1":
+* 1: Standard
+* 2: Vertebrate Mitochondrial
+* 3: Yeast Mitochondrial
+* 4: Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
+* 5: Invertebrate Mitochondrial
+* 6: Ciliate Macronuclear and Dasycladacean
+* 9: Echinoderm Mitochondrial
+* 10: ALternative Ciliate Macronuclear
+* 11: Eubacterial
+* 12: Alternative Yeast
+* 13: Ascidian Mitochondrial
+* 14: Flatworm Mitochondrial
+* 15: Blepharisma Nuclear Code
+
+
+
+## Contributing
+
+1. Fork it ( http://github.com/proxhotdog/CodonUsage/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/lib/CodonUsage/kazusaDB.rb

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+require "open-uri"
+require "csv"
+require "json"
+
+module CodonUsage
+    class KazusaDB
+        def initialize(host: "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=", aa: "1", species: "9606")
+            #1: Standard
+            #2: Vertebrate Mitochondrial
+            #3: Yeast Mitochondrial
+            #4: Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
+            #5: Invertebrate Mitochondrial
+            #6: Ciliate Macronuclear and Dasycladacean
+            #9: Echinoderm Mitochondrial
+            #10: ALternative Ciliate Macronuclear
+            #11: Eubacterial
+            #12: Alternative Yeast
+            #13: Ascidian Mitochondrial
+            #14: Flatworm Mitochondrial
+            #15: Blepharisma Nuclear Code
+            @url = "#{host}#{species}&aa=#{aa}&style=N"
+            @codonTable = {}
+        end
+
+        def getURL
+            return @url
+        end
+
+        def fetch
+            tableString = ""
+            codonTable = {}
+            codonList = []
+            prefList = []
+            open(@url) {|url|
+                url.each_line {|line| 
+                    tableString<<line.gsub(/\( +/, '').gsub(/\)[ |\n]/, "\n").gsub(/ +/, "\t").gsub(/\n\t/,"\n") if line.match(/^[A|U|G|C]{3}/)
+                }
+            }
+            CSV.parse(tableString, {:col_sep => "\t"}).each {|codon|
+                codonList.push(codon[0])
+                prefList.push(codon[2])
+            }
+            @codonTable = Hash[codonList.zip(prefList)]
+            return @codonTable
+        end
+
+        def getHash
+            fetch
+            return @codonTable
+        end
+
+        def to_json
+            fetch
+            return @codonTable.to_json
+        end
+    end
+end

data/lib/CodonUsage/version.rb

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+module CodonUsage
+  VERSION = "0.0.1"
+end

data/lib/CodonUsage.rb

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+require "CodonUsage/version"
+require "CodonUsage/kazusaDB"
+
+module CodonUsage
+#        URL = "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species="
+#        def self.get_URL
+#            return URL
+#        end
+    # Your code goes here...
+end

data/spec/CodonUsage_spec.rb

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+system("clear")
+puts "Rspec results"
+puts "================="
+require 'CodonUsage'
+require 'spec_helper'
+
+describe CodonUsage::KazusaDB do
+    #let(:dblink) {"http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species="}
+    it "Create object using default args" do
+        CodonUsage::KazusaDB.new.getURL.should == "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606&aa=1&style=N"
+    end
+    it "#aa 2" do
+        CodonUsage::KazusaDB.new(aa: "2").getURL.should == "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606&aa=2&style=N"
+    end
+    it "#species:Mycobacterium tuberculosis H37Rv" do
+        CodonUsage::KazusaDB.new(species: "83332").getURL.should == "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=83332&aa=1&style=N"
+    end
+    it "#getHash working?" do
+        p CodonUsage::KazusaDB.new(species: "83332").getHash
+    end
+    it "#to_json working?" do
+        p CodonUsage::KazusaDB.new(species: "83332").to_json
+    end
+end

data/spec/spec_helper.rb

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+RSpec.configure do |config|
+    config.color_enabled = true
+    config.tty = true
+    config.formatter = :documentation
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: CodonUsage
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- proxhotdog
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-02-18 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.14'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.14'
+description: A ruby gem that parses codon table from http://www.kazusa.or.jp/codon
+  and turn it to hash or JSON
+email:
+- hotdogcheng@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- CodonUsage.gemspec
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/CodonUsage.rb
+- lib/CodonUsage/kazusaDB.rb
+- lib/CodonUsage/version.rb
+- spec/CodonUsage_spec.rb
+- spec/spec_helper.rb
+homepage: ''
+licenses:
+- GPLv3
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: A ruby gem that parses codon table from http://www.kazusa.or.jp/codon
+test_files:
+- spec/CodonUsage_spec.rb
+- spec/spec_helper.rb