vienna_rna 0.1.1 → 0.1.2

data/lib/modules/fftbor.rb

@@ -3,6 +3,28 @@ require "bigdecimal"
 
 module ViennaRna
   class Fftbor < Xbor
+    MODES = {
+      dispatch:   "TripletPF",
+      standalone: "Fftbor"
+    }
+    
+    def run_command(flags = {})
+      flags = { mode: :dispatch }.merge(flags)
+      
+      ap flags
+      
+      unless MODES[flags[:mode]]
+        STDERR.puts "ERROR: The mode requested (%s) is not available" % flags[:mode]
+      end
+      
+      case flags[:mode]
+      when :standalone then
+        super(flags)
+      when :dispatch then
+        "./%s -m 6 -tr 0 -s %s -ss '%s'" % [MODES[flags[:mode]], data.seq, data.safe_structure]
+      end
+    end
+    
     def partition
       response.split(/\n/).find { |line| line =~ /^Scaling factor.*:\s+(\d+\.\d+)/ }
       BigDecimal.new($1)

data/lib/modules/rnabor.rb

@@ -12,7 +12,7 @@ module ViennaRna
     end
     
     def counts
-      (non_zero_counts = self.class.parse(response).map { |row| row[2].to_i }) + [0] * (data.seq.length - non_zero_counts.length + 1)
+      (non_zero_counts = self.class.parse(response).map { |row| BigDecimal.new(row[2]).to_i }) + [0] * (data.seq.length - non_zero_counts.length + 1)
     end
     
     def distribution(options = {})

data/lib/modules/xbor.rb

@@ -15,7 +15,7 @@ module ViennaRna
     end
     
     def self.parse(response)
-      response.split(/\n/).select { |line| line =~ /^\d+\t\d+/ }.map { |line| line.split(/\t/) }
+      response.split(/\n/).select { |line| line =~ /^\d+\t-?\d+/ }.map { |line| line.split(/\t/) }
     end
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-26 00:00:00.000000000 Z
+date: 2012-06-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio