vienna_rna 0.0.0
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- data/lib/modules/base.rb +51 -0
- data/lib/modules/batch.rb +1 -0
- data/lib/modules/fold.rb +7 -0
- data/lib/modules/utils.rb +12 -0
- data/lib/vienna_rna.rb +19 -0
- metadata +76 -0
data/lib/modules/base.rb
ADDED
@@ -0,0 +1,51 @@
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module ViennaRna
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class Base
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class_inheritable_accessor :exec_name
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4
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class << self
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6
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def method_added(name)
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7
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if name == :run
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8
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unless @chaining
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9
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@chaining = true
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alias_method_chain :run, :hooks
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else
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remove_instance_variable(:@chaining)
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end
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end
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end
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def exec_exists?(name)
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!%x[which rna#{name.to_s.downcase}].empty?
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end
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end
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22
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attr_reader :fasta
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def exec_name
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@exec_name || "rna#{self.class.name.split('::').last.underscore}"
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end
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def initialize(fasta)
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@fasta = fasta
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end
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def run_with_hooks(flags = {})
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pre_run_check
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run_without_hooks
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end
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def pre_run_check
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if self.class.exec_exists?(exec_name)
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raise RuntimeError.new("#{exec_name} is not defined on this machine")
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end
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end
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42
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def stringify_flags(flags)
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flags.inject("") { |string, flag| (string + (" %s %s" % flag)).strip }
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end
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def run(flags = {})
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%x[echo #{fasta.seq} | #{exec_name} #{stringify_flags(flags)}]
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end
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end
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51
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end
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@@ -0,0 +1 @@
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1
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# This should be a meta-overlord class that runs the same command on a collection of subclasses of base.rb
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data/lib/modules/fold.rb
ADDED
data/lib/vienna_rna.rb
ADDED
@@ -0,0 +1,19 @@
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require "bio"
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require "active_support/inflector"
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require "active_support/core_ext/class"
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require "active_support/core_ext/module"
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# Clean up this include order.
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Dir[File.join(File.dirname(__FILE__), "/modules/*")].each do |file|
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require file
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end
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module ViennaRna
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def self.const_missing(name)
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if Base.exec_exists?(name)
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module_eval do
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const_set(name, Class.new(Base))
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end
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end
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end
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end
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metadata
ADDED
@@ -0,0 +1,76 @@
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1
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--- !ruby/object:Gem::Specification
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name: vienna_rna
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version: !ruby/object:Gem::Version
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version: 0.0.0
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prerelease:
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platform: ruby
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authors:
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- Evan Senter
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2012-03-26 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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requirement: &70112760171500 !ruby/object:Gem::Requirement
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none: false
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requirements:
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19
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: *70112760171500
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25
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- !ruby/object:Gem::Dependency
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name: active_support
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requirement: &70112760171060 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: *70112760171060
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description: A Ruby API for interacting with the Vienna RNA package.
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email: evansenter@gmail.com
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executables: []
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extensions: []
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extra_rdoc_files: []
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files:
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- !binary |-
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Li9saWIvbW9kdWxlcy9iYXNlLnJi
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- !binary |-
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45
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Li9saWIvbW9kdWxlcy9iYXRjaC5yYg==
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46
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- !binary |-
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47
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Li9saWIvbW9kdWxlcy9mb2xkLnJi
|
48
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- !binary |-
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49
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Li9saWIvbW9kdWxlcy91dGlscy5yYg==
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- !binary |-
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51
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Li9saWIvdmllbm5hX3JuYS5yYg==
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homepage: http://rubygems.org/gems/vienna_rna
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licenses: []
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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66
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requirements:
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67
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
|
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rubyforge_project:
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rubygems_version: 1.8.11
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signing_key:
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specification_version: 3
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summary: Bindings to the Vienna RNA package.
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test_files: []
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