vienna_rna 0.0.6 → 0.1.0

data/lib/modules/fftbor.rb

@@ -1,48 +1,33 @@
+require "tempfile"
+
 module ViennaRna
   class Fftbor < Base
-    attr_reader :flags
-    
     def run_command(flags)
-      @flags = flags
+      file = Tempfile.new("rna")
+      file.write("%s\n" % data.seq)
+      file.write("%s\n" % data.safe_structure)
+      file.close
       
-      "./FFTbor -s %s -r %s -c %s -p %s" % [
-        data.seq, 
-        data.safe_structure,
-        flags[:scaling_factor] ||= 1,
-        flags[:precision] ||= 6
-      ]
-    end
-    
-    def parse_partition
-      response.split(/\n/).find { |line| line =~ /^Z\[1\]\[\d+\]:/ }.match(/^Z\[1\]\[\d+\]:\s*(.*)/)[1].to_f
+      "./FFTbor %s" % file.path
     end
     
-    def parse_total_count
-      response.split(/\n/).find { |line| line =~ /^Z\[\d+\]\[1\]:/ }.match(/^Z\[\d+\]\[1\]:\s*(.*)/)[1].to_i
+    def partition
+      # Scaling factor (Z{1, n}): 586.684
+      response.split(/\n/).find { |line| line =~ /^Scaling factor.*:\s+(\d+\.\d+)/ }
+      $1.to_f
     end
     
-    def parse_points
-      self.class.parse(response, "ROOTS AND SOLUTIONS") { |line| line.strip.split(/\s\s+/).map { |value| eval("Complex(#{value})") } }
+    def total_count
+      response.split(/\n/).find { |line| line =~ /^Number of structures: (\d+)/ }
+      $1.to_i
     end
     
-    def parse_distribution
-      if flags[:scaling_factor] != 1
-        puts "Warning: The scaling factor was set to #{flags[:scaling_factor]}. The Boltzmann distribution is not setup to handle scaling in this fashion."
-      end
-      
-      self.class.parse(response, "DISTRIBUTION") { |line| line.strip.split(/:\s*/).last.to_f }
+    def distribution
+      self.class.parse(response).map { |row| row[1].to_f }
     end
     
-    def self.parse(response, delimiter)
-      response.split(/\n/).reject do |line| 
-        line.empty?
-      end.drop_while do |line|
-        line !~ /^START #{delimiter}/i
-      end.reverse.drop_while do |line|
-        line !~ /^END #{delimiter}/i
-      end.reverse[1..-2].map do |line|
-        yield line
-      end
+    def self.parse(response)
+      response.split(/\n/).select { |line| line =~ /^\d+\t\d+(\.\d+)?/ }.map { |line| line.split(/\t/) }
     end
   end
 end

data/lib/modules/rnabor.rb

@@ -8,26 +8,26 @@ module ViennaRna
       file.write("%s\n" % data.safe_structure)
       file.close
       
-      "./RNAbor %s" % file.path
+      "./RNAbor -nodangle %s" % file.path
     end
     
-    def parse_partition
-      parse_non_zero_shells.sum
+    def partition
+      non_zero_shells.sum
     end
     
-    def parse_total_count
-      parse_counts.sum
+    def total_count
+      counts.sum
     end
     
-    def parse_counts
+    def counts
       (non_zero_counts = self.class.parse(response).map { |row| row[2].to_i }) + [0] * (data.seq.length - non_zero_counts.length + 1)
     end
     
-    def parse_distribution
-      (non_zero_distribution = parse_non_zero_shells.map { |i| i / parse_partition }) + [0.0] * (data.seq.length - non_zero_distribution.length + 1)
+    def distribution
+      (non_zero_distribution = non_zero_shells.map { |i| i / partition }) + [0.0] * (data.seq.length - non_zero_distribution.length + 1)
     end
     
-    def parse_non_zero_shells
+    def non_zero_shells
       self.class.parse(response).map { |row| row[1].to_f }
     end
     

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.1.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-26 00:00:00.000000000 Z
+date: 2012-06-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio