CodonUsage 0.0.3 → 0.0.4

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: e98fa638049cf13652967c4d3c6440c713b36a1b
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data/CodonUsage.gemspec

@@ -10,8 +10,8 @@ Gem::Specification.new do |spec|
   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      = "https://github.com/proxhotdog/CodonTable"
-  spec.license       = "GPLv3"
+  spec.homepage      = "https://github.com/proxhotdog/CodonUsage"
+  spec.license       = "GPL v3"
 
   spec.files         = `git ls-files -z`.split("\x0")
   spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }

data/Gemfile

@@ -1,4 +1,4 @@
 source 'https://rubygems.org'
-gem "CodonTable", :git => "git://github.com/proxhotdog/codonTable.git"
+gem "CodonTable", :git => "git://github.com/proxhotdog/CodonUsage.git"
 # Specify your gem's dependencies in CodonUsage.gemspec
 gemspec

data/LICENSE.txt

@@ -1,22 +1,3 @@
 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.
+GPL v3

data/README.md

@@ -1,8 +1,8 @@
 # CodonUsage
-A ruby gem that parses Codon Usage table provided by: http://www.kazusa.or.jp/codon/ that output the information in a hash or JSON forma formatt
+A ruby gem that parses Codon Usage table provided by: http://www.kazusa.or.jp/codon/ that output the information in a hash or JSON format. You can find this gem on http://rubygems.org/gems/CodonUsage
 
 ## Version
-    0.0.3
+    0.0.4
 
 ## Disclaimer
 I write this gem because bioruby doesn't provide any library for me to do this job, and this is my first ruby gem. Hope this gem can help people in the bioinformatics field! :)
@@ -23,7 +23,7 @@ I write this gem because bioruby doesn't provide any library for me to do this j
 
 for the argument "species", default value = "9606" which is the ID of Homo sapiens (Human).
 
-for the arguement "aa", it is the genetic code, default value = "1":
+for the arguement "aa", it is the genetic code, default value = "1", for other values, please refer to the following list:
 * 1: Standard
 * 2: Vertebrate Mitochondrial
 * 3: Yeast Mitochondrial

data/lib/CodonUsage/kazusaDB.rb

@@ -8,20 +8,7 @@ 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
+        def initialize(host: "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=", aa: "1", species: "9606") # for default values of the arugments, please refer to README.md
             @url = "#{host}#{species}&aa=#{aa}&style=N"
             @codonPreferenceTable = {}
             @codonTable = {}

data/lib/CodonUsage/version.rb

@@ -1,3 +1,3 @@
 module CodonUsage
-  VERSION = "0.0.3"
+  VERSION = "0.0.4"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: CodonUsage
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors:
 - proxhotdog
@@ -57,9 +57,9 @@ files:
 - lib/CodonUsage/version.rb
 - spec/CodonUsage_spec.rb
 - spec/spec_helper.rb
-homepage: https://github.com/proxhotdog/CodonTable
+homepage: https://github.com/proxhotdog/CodonUsage
 licenses:
-- GPLv3
+- GPL v3
 metadata: {}
 post_install_message: 
 rdoc_options: []