codon_table_parser 0.2.0 → 0.2.2

data/README.md

@@ -6,7 +6,7 @@ The output can be easily customized and used to update the respective constants
 ## Installation
 
 ``` bash
-gem install codon_table_parser
+$ gem install codon_table_parser
 
 ```
 

data/lib/codon_table_parser.rb

@@ -1,8 +1,8 @@
 # encoding: utf-8
 
-# Parses the NCBI genetic code table, generating separate hash maps of each species' name, start & stop codons and codon table.  
+# Parses the NCBI genetic code table, generating separate hash maps of each species' name, start & stop codons and codon table.
 #
-# to return definitions, start  & stop codons as well as codon tables that can be used 
+# to return definitions, start  & stop codons as well as codon tables that can be used
 class CodonTableParser
 
   attr_reader :address
@@ -46,9 +46,8 @@ class CodonTableParser
     arr
   end
 
-  def parse data 
-    del       = /.*?\s/.source               # .+ does not work as the regex is greedy.
-    # del       = /.*?(?=[a-z])/.source        # Using non-greedy search + pos. lookahead also works        
+  def parse data
+    del       = /.*?/.source
     l_name    = /name "(.*?)"#{del}/.source
     s_name    = /(|name ".*?"#{del})/.source # Either nothing 'line does not exists' or the short name.
     id        = /id (\d+)#{del}/.source
@@ -56,7 +55,7 @@ class CodonTableParser
     sncbieaa  = /sncbieaa "(.*?)"/.source
 
     # flag 'o':
-    # Perform inline substitutions (#{variable}) only once on creation. 
+    # Perform inline substitutions (#{variable}) only once on creation.
     # Normally, the variable is inserted on every evaluation.
     result = data.scan(/#{l_name}#{s_name}#{id}#{ncbieaa}#{sncbieaa}/mo).
     inject([]) do |res, (l_name, s_name, id, ncbieaa, sncbieaa)|
@@ -64,7 +63,7 @@ class CodonTableParser
       short  = s_name.match(/[A-Z]{3}\d/)[0] unless s_name.empty?
       l_name = l_name.gsub(/\n/,'')
 
-      res << {:id         => id.to_i, 
+      res << {:id         => id.to_i,
               :long_name  => l_name,
               :short_name => short,
               :ncbieaa    => ncbieaa,
@@ -88,7 +87,7 @@ class CodonTableParser
   end
 
   def starts options = {}
-    Hash[@parsed_data.map do |species| 
+    Hash[@parsed_data.map do |species|
       codons = []
       species[:sncbieaa].split(//).each_with_index do |pos, i|
         if pos == 'M'
@@ -167,7 +166,7 @@ class CodonTableParser
 
   def custom_codons options, codons
     opt = options
-    if opt 
+    if opt
       codons = codons | opt[:add] if opt[:add]
       codons = codons.delete_if {|codon| opt[:remove].include?(codon)} if opt[:remove]
     end

data/lib/codon_table_parser/version.rb

@@ -1,3 +1,3 @@
 class CodonTableParser
-  VERSION = "0.2.0"
+  VERSION = "0.2.2"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: codon_table_parser
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-11-03 00:00:00.000000000Z
+date: 2012-01-18 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &13232540 !ruby/object:Gem::Requirement
+  requirement: &12020420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,7 +21,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *13232540
+  version_requirements: *12020420
 description: ! '   Parses the NCBI genetic code table, generating hash maps of each
   species'' name, start codons, stop codons and codon table. The output of CodonTableParser
   can be customized easily and used to update the respective constants of BioRuby''s
@@ -58,7 +58,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: codon_table_parser
-rubygems_version: 1.8.10
+rubygems_version: 1.8.11
 signing_key: 
 specification_version: 3
 summary: Parses the NCBI genetic code table, generating hash maps of each species'