CodonUsage 0.0.2 → 0.0.3

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@@ -1,7 +1,7 @@
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data/README.md

@@ -1,5 +1,14 @@
 # CodonUsage
-A ruby gem that parse Codon Usage table provided by: http://www.kazusa.or.jp/codon/
+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
+
+## Version
+    0.0.3
+
+## 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! :)
+
+## Before start
+    * Please use Ruby 1.9.3 or above
 
 ## Installation
     $ gem install CodonUsage
@@ -10,10 +19,11 @@ A ruby gem that parse Codon Usage table provided by: http://www.kazusa.or.jp/cod
     p foo.getURL
     p foo.getHash
     p foo.to_json
+    p foo.getCodonTable
 
-for species, "9606" is homo sapiens ID.
+for the argument "species", default value = "9606" which is the ID of Homo sapiens (Human).
 
-for aa, it is the codon translation table, default = "1":
+for the arguement "aa", it is the genetic code, default value = "1":
 * 1: Standard
 * 2: Vertebrate Mitochondrial
 * 3: Yeast Mitochondrial
@@ -28,7 +38,6 @@ for aa, it is the codon translation table, default = "1":
 * 14: Flatworm Mitochondrial
 * 15: Blepharisma Nuclear Code
 
-
 ## Contributing
 
 1. Fork it ( http://github.com/proxhotdog/CodonUsage/fork )

data/lib/CodonUsage/kazusaDB.rb

@@ -1,3 +1,7 @@
+#Author: proxhotdog
+#Email: hotdogcheng@gmail.com
+#License: GPL v3
+
 require "open-uri"
 require "csv"
 require "json"
@@ -19,6 +23,7 @@ module CodonUsage
             #14: Flatworm Mitochondrial
             #15: Blepharisma Nuclear Code
             @url = "#{host}#{species}&aa=#{aa}&style=N"
+            @codonPreferenceTable = {}
             @codonTable = {}
         end
 
@@ -31,27 +36,35 @@ module CodonUsage
             codonTable = {}
             codonList = []
             prefList = []
+            aminoAcidList = []
             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}/)
+                    tableString<<line.gsub(/\( +/, '').gsub(/\)[ |\n]/, "\n").gsub(/ +/, "\t").gsub(/\n\t/,"\n") if line.match(/^[A|U|G|C]{3}/) # Quick & dirty way to change that table to tab-delimited format just like CSV file
                 }
             }
             CSV.parse(tableString, {:col_sep => "\t"}).each {|codon|
-                codonList.push(codon[0])
-                prefList.push(codon[2])
+                codonList.push(codon[0]) # extract the triplet
+                prefList.push(codon[2]) # extract the fraction, also known as codon preference
+                aminoAcidList.push(codon[1]) # extract the coding amino acid since different organisms have different codon table
             }
-            @codonTable = Hash[codonList.zip(prefList)]
+            @codonPreferenceTable = Hash[codonList.zip(prefList)]
+            @codonTable = Hash[codonList.zip(aminoAcidList)]
+            return 0
+        end
+
+        def getCodonTable
+            fetch
             return @codonTable
         end
 
         def getHash
             fetch
-            return @codonTable
+            return @codonPreferenceTable
         end
 
         def to_json
             fetch
-            return @codonTable.to_json
+            return @codonPreferenceTable.to_json # just simply use built-in json library, only available Ruby 1.9.3+
         end
     end
 end

data/lib/CodonUsage/version.rb

@@ -1,3 +1,3 @@
 module CodonUsage
-  VERSION = "0.0.2"
+  VERSION = "0.0.3"
 end

data/spec/CodonUsage_spec.rb

@@ -23,4 +23,7 @@ describe CodonUsage::KazusaDB do
     it "#to_json working?" do
         p CodonUsage::KazusaDB.new(species: "83332").to_json
     end
+    it "#getCodonTable working?" do
+        p CodonUsage::KazusaDB.new(species: "83332").getCodonTable
+    end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: CodonUsage
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors:
 - proxhotdog