vienna_rna 0.0.0

data/lib/modules/base.rb

@@ -0,0 +1,51 @@
+module ViennaRna
+  class Base
+    class_inheritable_accessor :exec_name
+    
+    class << self
+      def method_added(name)
+        if name == :run
+          unless @chaining
+            @chaining = true
+            alias_method_chain :run, :hooks
+          else
+            remove_instance_variable(:@chaining)
+          end
+        end
+      end
+      
+      def exec_exists?(name)
+        !%x[which rna#{name.to_s.downcase}].empty?
+      end
+    end
+    
+    attr_reader :fasta
+    
+    def exec_name
+      @exec_name || "rna#{self.class.name.split('::').last.underscore}"
+    end
+    
+    def initialize(fasta)
+      @fasta = fasta
+    end
+    
+    def run_with_hooks(flags = {})
+      pre_run_check
+      run_without_hooks
+    end
+    
+    def pre_run_check
+      if self.class.exec_exists?(exec_name)
+        raise RuntimeError.new("#{exec_name} is not defined on this machine")
+      end
+    end
+    
+    def stringify_flags(flags)
+      flags.inject("") { |string, flag| (string + (" %s %s" % flag)).strip }
+    end
+    
+    def run(flags = {})
+      %x[echo #{fasta.seq} | #{exec_name} #{stringify_flags(flags)}]
+    end
+  end
+end

data/lib/modules/batch.rb

@@ -0,0 +1 @@
+# This should be a meta-overlord class that runs the same command on a collection of subclasses of base.rb

data/lib/modules/fold.rb

@@ -0,0 +1,7 @@
+# Rip this out, infer it through metaprogramming.
+
+module ViennaRna
+  class Fold < Base
+    
+  end
+end

data/lib/modules/utils.rb

@@ -0,0 +1,12 @@
+# "/Users/evansenter/Source/mirna_5.1/hairpin.fa"
+
+module ViennaRna
+  module Utils
+    class << self
+      def fastas_from_file(path)
+        # Force it to not be lazy.
+        Bio::FlatFile.auto(path).to_enum.map { |fasta| fasta }
+      end
+    end
+  end
+end

data/lib/vienna_rna.rb

@@ -0,0 +1,19 @@
+require "bio"
+require "active_support/inflector"
+require "active_support/core_ext/class"
+require "active_support/core_ext/module"
+
+# Clean up this include order.
+Dir[File.join(File.dirname(__FILE__), "/modules/*")].each do |file|
+  require file
+end
+
+module ViennaRna
+  def self.const_missing(name)
+    if Base.exec_exists?(name)
+      module_eval do
+        const_set(name, Class.new(Base))
+      end
+    end
+  end
+end

metadata

@@ -0,0 +1,76 @@
+--- !ruby/object:Gem::Specification
+name: vienna_rna
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+  prerelease: 
+platform: ruby
+authors:
+- Evan Senter
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-03-26 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &70112760171500 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *70112760171500
+- !ruby/object:Gem::Dependency
+  name: active_support
+  requirement: &70112760171060 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *70112760171060
+description: A Ruby API for interacting with the Vienna RNA package.
+email: evansenter@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- !binary |-
+  Li9saWIvbW9kdWxlcy9iYXNlLnJi
+- !binary |-
+  Li9saWIvbW9kdWxlcy9iYXRjaC5yYg==
+- !binary |-
+  Li9saWIvbW9kdWxlcy9mb2xkLnJi
+- !binary |-
+  Li9saWIvbW9kdWxlcy91dGlscy5yYg==
+- !binary |-
+  Li9saWIvdmllbm5hX3JuYS5yYg==
+homepage: http://rubygems.org/gems/vienna_rna
+licenses: []
+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: 1.8.11
+signing_key: 
+specification_version: 3
+summary: Bindings to the Vienna RNA package.
+test_files: []