vienna_rna 0.5.5 → 0.6.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: dcf9b4f4f050e4ca03f152385f663d8e6add6d66
+  metadata.gz: 16cb73b2fcfe880d27bc3754363cb986f12b9e93
+  data.tar.gz: a18ea5d222722e5512e8d46b3ecdb4a837c44bf8
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+  data.tar.gz: 83153eae6e5c83f85cb30772ac1ae3134a99c226e4e84cd0a96ad1157087a633ef54cb66b5402bb99095d685bde334d7703c4fbf7738a9c8a964de8b98e10d9e

data/lib/vienna_rna/modules/base.rb

@@ -40,10 +40,6 @@ module ViennaRna
           end
         end
       end
-      
-      def debugger
-        STDERR.puts yield if ViennaRna.debug
-      end
     end
     
     attr_reader :data, :response, :runtime
@@ -86,7 +82,7 @@ module ViennaRna
             post_process if respond_to?(:post_process)
           end
         
-          debugger { "Total runtime: %.3f sec." % runtime.real }
+          ViennaRna.debugger { "Total runtime: %.3f sec." % runtime.real }
         end
       else
         self
@@ -114,7 +110,7 @@ module ViennaRna
         "echo #{exec_sequence_format} | #{exec_name} #{stringify_flags(flags)}"
       end
       
-      debugger { command }
+      ViennaRna.debugger { command }
         
       %x[#{command}]
     end

data/lib/vienna_rna/modules/rna.rb

@@ -18,7 +18,8 @@ module ViennaRna
       end
       
       def init_from_fasta(string)
-        init_from_string(*string.split(/\n/).reject { |line| line.start_with?(">") })
+        string = File.read(string).chomp if File.exist?(string)
+        init_from_string(*string.split(/\n/).reject { |line| line.start_with?(">") }[0, 2])
       end
     
       def init_from_self(rna)
@@ -35,6 +36,10 @@ module ViennaRna
       when :mfe   then ViennaRna::Fold.run(Rna.init_from_string(seq)).structure
       when String then structure
       end
+
+      if str && seq.length != str.length
+        ViennaRna.debugger { "The sequence length (%d) doesn't match the structure length (%d)" % [seq.length, str.length] }
+      end
     end
     
     alias :seq :sequence

data/lib/vienna_rna/modules/xbor.rb

@@ -15,7 +15,7 @@ module ViennaRna
       file.write("%s\n" % data.str)
       file.close
       
-      debugger { "Running FFTbor on #{data.inspect}" }
+      ViennaRna.debugger { "Running FFTbor on #{data.inspect}" }
       
       "%s %s %s" % [
         exec_name, 

data/lib/vienna_rna.rb

@@ -28,6 +28,10 @@ module ViennaRna
       end
     end
   end
+
+  def self.debugger
+    STDERR.puts yield if ViennaRna.debug
+  end
   
   def self.debug
     @debug
@@ -41,6 +45,14 @@ end
 # This dirties up the public namespace, but I use it so many times that I want a shorthand to it
 unless defined? RNA
   def RNA(sequence, structure = nil)
-    ViennaRna::Rna.init_from_string(sequence, structure)
+    RNA.from_string(sequence, structure)
+  end
+end
+
+module RNA
+  def self.method_missing(name, *args, &block)
+    if "#{name}" =~ /^from_\w+$/
+      ViennaRna::Rna.send("init_#{name}", *args)
+    else super end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.5.5
+  version: 0.6.0
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-10 00:00:00.000000000 Z
+date: 2013-07-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -138,7 +138,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.0.5
 signing_key: 
 specification_version: 4
 summary: Bindings to the Vienna RNA package.