rbfam 0.1.1 → 0.1.3

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 69c97958b2246fffbb4915ee3d60bcd5161c15dd
+  data.tar.gz: 6cbba5157ab211ee188328d1fed2a6b83a07f32b
+SHA512:
+  metadata.gz: 81d8588a7aae75b41d777409740a0db75107ec0b7e5ba059110511da286fc50c1c40314c8471120a862e73e27657146ca37dd8db4f62b70d7d8b02a198526511
+  data.tar.gz: d07932c2d7981fa90f9146554a4c81cdd5497e367c870d13f40bae445bb422affb904a13fef6caaab559fd130d633cf35e5891e9d4a2e2ac8ed412d0122fb7c0

data/lib/rbfam/helpers/simple_names.json

@@ -0,0 +1,11 @@
+{
+  "purine":       "RF00167",
+  "tpp":          "RF00059",
+  "secis_1":      "RF00031",
+  "trna":         "RF00005",
+  "let_7":        "RF00027",
+  "snora71":      "RF00056",
+  "u7":           "RF00066",
+  "rose":         "RF00435",
+  "hammerhead_3": "RF00008"
+}

data/lib/rbfam/modules/family.rb

@@ -2,22 +2,21 @@ module Rbfam
   class Family
     include Rbfam::CommonHelpers
     
-    attr_reader :family_name
+    attr_reader :family_name, :description
     
     class << self
-      def purine;       new("RF00167"); end
-      def tpp;          new("RF00059"); end
-      def secis_1;      new("RF00031"); end
-      def trna;         new("RF00005"); end
-      def let_7;        new("RF00027"); end
-      def snora71;      new("RF00056"); end
-      def u7;           new("RF00066"); end
-      def rose;         new("RF00435"); end
-      def hammerhead_3; new("RF00008"); end
+      def method_missing(name, *args, &block)
+        READABLE[name.to_s] ? new(READABLE[name.to_s]) : super
+      end
     end
     
-    def initialize(family_name)
+    def initialize(family_name, description = "")
       @family_name = family_name
+      @description = description
+    end
+    
+    def id
+      ("%s %s" % [family_name, description.downcase]).strip.gsub(/\W+/, "_")
     end
     
     def alignment

data/lib/rbfam.rb

@@ -1,3 +1,4 @@
+require "json"
 require "bio"
 require "vienna_rna"
 require "entrez"
@@ -12,4 +13,6 @@ module Rbfam
   def self.script(name)
     require "rbfam/scripts/#{File.basename(name, '.rb')}"
   end
-end
+end
+
+Rbfam::Family.const_set(:READABLE, JSON.parse(File.read(File.join(File.dirname(__FILE__), "rbfam", "helpers", "simple_names.json"))))

metadata

@@ -1,78 +1,69 @@
 --- !ruby/object:Gem::Specification
 name: rbfam
 version: !ruby/object:Gem::Version
-  version: 0.1.1
-  prerelease: 
+  version: 0.1.3
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-06 00:00:00.000000000 Z
+date: 2013-04-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: entrez
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.5.8.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.5.8.1
 - !ruby/object:Gem::Dependency
   name: httparty
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.8.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.8.3
 - !ruby/object:Gem::Dependency
   name: vienna_rna
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.1.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 0.1.3
 description: Light wrapper for RFam data in Ruby.
@@ -82,6 +73,7 @@ extensions: []
 extra_rdoc_files: []
 files:
 - lib/rbfam/helpers/common.rb
+- lib/rbfam/helpers/simple_names.json
 - lib/rbfam/modules/alignment.rb
 - lib/rbfam/modules/family.rb
 - lib/rbfam/modules/sequence.rb
@@ -91,26 +83,25 @@ files:
 - README.md
 homepage: http://rubygems.org/gems/rbfam
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.0.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Bindings to Rfam.
 test_files: []