vienna_rna 0.5.5 → 0.6.0

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  SHA1:
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  SHA512:
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@@ -40,10 +40,6 @@ module ViennaRna
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  end
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  end
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  end
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-
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- def debugger
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- STDERR.puts yield if ViennaRna.debug
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- end
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  end
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  attr_reader :data, :response, :runtime
@@ -86,7 +82,7 @@ module ViennaRna
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  post_process if respond_to?(:post_process)
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  end
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- debugger { "Total runtime: %.3f sec." % runtime.real }
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+ ViennaRna.debugger { "Total runtime: %.3f sec." % runtime.real }
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  end
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  else
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  self
@@ -114,7 +110,7 @@ module ViennaRna
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  "echo #{exec_sequence_format} | #{exec_name} #{stringify_flags(flags)}"
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  end
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- debugger { command }
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+ ViennaRna.debugger { command }
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  %x[#{command}]
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  end
@@ -18,7 +18,8 @@ module ViennaRna
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  end
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  def init_from_fasta(string)
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- init_from_string(*string.split(/\n/).reject { |line| line.start_with?(">") })
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+ string = File.read(string).chomp if File.exist?(string)
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+ init_from_string(*string.split(/\n/).reject { |line| line.start_with?(">") }[0, 2])
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  end
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  def init_from_self(rna)
@@ -35,6 +36,10 @@ module ViennaRna
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  when :mfe then ViennaRna::Fold.run(Rna.init_from_string(seq)).structure
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  when String then structure
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  end
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+
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+ if str && seq.length != str.length
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+ ViennaRna.debugger { "The sequence length (%d) doesn't match the structure length (%d)" % [seq.length, str.length] }
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+ end
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  end
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  alias :seq :sequence
@@ -15,7 +15,7 @@ module ViennaRna
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  file.write("%s\n" % data.str)
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  file.close
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- debugger { "Running FFTbor on #{data.inspect}" }
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+ ViennaRna.debugger { "Running FFTbor on #{data.inspect}" }
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  "%s %s %s" % [
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  exec_name,
data/lib/vienna_rna.rb CHANGED
@@ -28,6 +28,10 @@ module ViennaRna
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  end
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  end
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  end
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+
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+ def self.debugger
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+ STDERR.puts yield if ViennaRna.debug
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+ end
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  def self.debug
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  @debug
@@ -41,6 +45,14 @@ end
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  # This dirties up the public namespace, but I use it so many times that I want a shorthand to it
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  unless defined? RNA
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  def RNA(sequence, structure = nil)
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- ViennaRna::Rna.init_from_string(sequence, structure)
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+ RNA.from_string(sequence, structure)
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+ end
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+ end
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+
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+ module RNA
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+ def self.method_missing(name, *args, &block)
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+ if "#{name}" =~ /^from_\w+$/
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+ ViennaRna::Rna.send("init_#{name}", *args)
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+ else super end
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  end
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  end
metadata CHANGED
@@ -1,14 +1,14 @@
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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: 0.5.5
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+ version: 0.6.0
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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: 2013-07-10 00:00:00.000000000 Z
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+ date: 2013-07-30 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio
@@ -138,7 +138,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 2.0.3
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+ rubygems_version: 2.0.5
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  signing_key:
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  specification_version: 4
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  summary: Bindings to the Vienna RNA package.