vienna_rna 0.0.1 → 0.0.2

data/lib/modules/base.rb

@@ -25,13 +25,16 @@ module ViennaRna
       @exec_name || "rna#{self.class.name.split('::').last.underscore}"
     end
     
-    def initialize(fasta)
-      @fasta = fasta
+    def initialize(data)
+      @fasta = case data
+      when Bio::FastaFormat then data
+      when String           then Bio::FastaFormat.new(data.split(/\n/).length > 1 ? data : ">\n%s" % data)
+      end
     end
     
     def run_with_hooks(flags = {})
       pre_run_check
-      response = run_without_hooks
+      response = run_without_hooks(flags)
       self.class.method_defined?(:post_process) ? post_process(response) : response  
     end
     
@@ -42,7 +45,7 @@ module ViennaRna
     end
     
     def stringify_flags(flags)
-      flags.inject("") { |string, flag| (string + (" %s %s" % flag)).strip }
+      flags.inject("") { |string, flag| (string + (" -%s %s" % flag)).strip }
     end
     
     def run(flags = {})

data/lib/modules/fold.rb

@@ -1,15 +1,24 @@
-# Rip this out, infer it through metaprogramming.
-
 module ViennaRna
   class Fold < Base
+    attr_reader :structure, :mfe
+    
     def post_process(response)
-      structure = response.split(/\n/).last.gsub(/ \(\s*-?\d*\.\d*\)$/, "")
+      tap do
+        structure = response.split(/\n/).last.gsub(/ \(\s*(-?\d*\.\d*)\)$/, "")
       
-      unless fasta.seq.length == structure.length
-        raise "Sequence: '#{fasta.seq}'\nStructure: '#{structure}'"
-      else
-        structure
+        unless fasta.seq.length == structure.length
+          raise "Sequence: '#{fasta.seq}'\nStructure: '#{structure}'"
+        else
+          @structure, @mfe = structure, $1
+        end
       end
     end
   end
+  
+  # Mix this baby into the Batch class after I write it for great cleanness!
+  module Batch
+    def prune_same_structures
+      
+    end
+  end
 end

data/lib/modules/subopt.rb

@@ -0,0 +1,19 @@
+module ViennaRna
+  class Subopt < Base
+    attr_reader :structures
+    
+    def post_process(response)
+      tap do
+        @structures = response.split(/\n/)
+      end
+    end
+    
+    def bin(count = 1)
+      run(p: count).structures.inject(Hash.new { |hash, key| hash[key] = 0 }) do |hash, structure|
+        hash.tap do
+          hash[structure] += 1
+        end
+      end
+    end
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors:
@@ -13,7 +13,7 @@ date: 2012-03-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &70224206504420 !ruby/object:Gem::Requirement
+  requirement: &70120459237640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70224206504420
+  version_requirements: *70120459237640
 - !ruby/object:Gem::Dependency
   name: active_support
-  requirement: &70224206503980 !ruby/object:Gem::Requirement
+  requirement: &70120459237200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,7 +32,7 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70224206503980
+  version_requirements: *70120459237200
 description: A Ruby API for interacting with the Vienna RNA package.
 email: evansenter@gmail.com
 executables: []
@@ -45,6 +45,8 @@ files:
   Li9saWIvbW9kdWxlcy9iYXRjaC5yYg==
 - !binary |-
   Li9saWIvbW9kdWxlcy9mb2xkLnJi
+- !binary |-
+  Li9saWIvbW9kdWxlcy9zdWJvcHQucmI=
 - !binary |-
   Li9saWIvbW9kdWxlcy91dGlscy5yYg==
 - !binary |-