vienna_rna 0.5.5 → 0.6.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/vienna_rna/modules/base.rb +2 -6
- data/lib/vienna_rna/modules/rna.rb +6 -1
- data/lib/vienna_rna/modules/xbor.rb +1 -1
- data/lib/vienna_rna.rb +13 -1
- metadata +3 -3
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 16cb73b2fcfe880d27bc3754363cb986f12b9e93
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4
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data.tar.gz: a18ea5d222722e5512e8d46b3ecdb4a837c44bf8
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 1e33cfffbe0538c3e6c887a8b18f65f9e74c2f26d1aa0255ffd079710770df8c4118804f9183969568cde1f65a703563a501cf899e136e312bc58e4bc0360c5c
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data.tar.gz: 83153eae6e5c83f85cb30772ac1ae3134a99c226e4e84cd0a96ad1157087a633ef54cb66b5402bb99095d685bde334d7703c4fbf7738a9c8a964de8b98e10d9e
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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
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@@ -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
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@@ -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
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@@ -18,7 +18,8 @@ module ViennaRna
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end
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def init_from_fasta(string)
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-
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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)
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@@ -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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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
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data/lib/vienna_rna.rb
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@@ -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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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
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@@ -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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-
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RNA.from_string(sequence, structure)
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end
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end
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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
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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.
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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-
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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
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@@ -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.
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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.
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