genevalidator 1.6.1 → 1.6.2

data/lib/genevalidator/validation_blast_reading_frame.rb

@@ -1,24 +1,29 @@
+require 'forwardable'
+
+require 'genevalidator/exceptions'
 require 'genevalidator/validation_report'
+require 'genevalidator/validation_test'
+
 module GeneValidator
   ##
   # Class that stores the validation output information
   class BlastRFValidationOutput < ValidationReport
-    attr_reader :frames_histo
+    attr_reader :frames
     attr_reader :msg
     attr_reader :total_hsp
     attr_reader :result
 
-    def initialize(short_header, header, description, frames_histo,
+    def initialize(short_header, header, description, frames,
                    expected = :yes)
       @short_header, @header, @description = short_header, header, description
-      @frames_histo = frames_histo
+      @frames = frames
       @expected     = expected
       @result       = validation
 
       @msg          = ''
       @exp_msg      = ''
       @total_hsp    = 0
-      @frames_histo.each do |x, y|
+      @frames.each do |x, y|
         @msg << "#{y}&nbsp;HSPs&nbsp;align&nbsp;in&nbsp;frame&nbsp;#{x}; "
         @exp_msg << "#{y} HSPs align in frame #{x}; "
         @total_hsp += y.to_i
@@ -36,7 +41,7 @@ module GeneValidator
       t = "BLAST identified #{@total_hsp} High-scoring Segment Pairs" \
              ' (HSPs)'
       if @result == :yes # i.e. if there is only one ORF...
-        frame = @frames_histo.keys[0].to_s
+        frame = @frames.keys[0].to_s
         t1    = "; all of these align in frame #{frame}."
       else
         t1 = ": #{@exp_msg.gsub(/; $/, '')}."
@@ -61,7 +66,7 @@ module GeneValidator
       # chack if there are different reading frames
       count_p = 0
       count_n = 0
-      frames_histo.each do |x, _y|
+      frames.each do |x, _y|
         count_p += 1 if x > 0
         count_n += 1 if x < 0
       end
@@ -75,7 +80,7 @@ module GeneValidator
   class BlastReadingFrameValidation < ValidationTest
     def initialize(type, prediction, hits = nil)
       super
-      @short_header = 'Frame'
+      @short_header = 'ReadingFrame'
       @header       = 'Reading Frame'
       @description  = 'Check whether there is a single reading frame among' \
                       ' BLAST hits. Otherwise there might be a reading frame' \
@@ -101,29 +106,25 @@ module GeneValidator
       start = Time.now
 
       rfs =  lst.map { |x| x.hsp_list.map(&:query_reading_frame) }.flatten
-      frames_histo = Hash[rfs.group_by { |x| x }.map { |k, vs| [k, vs.length] }]
+      frames = Hash[rfs.group_by { |x| x }.map { |k, vs| [k, vs.length] }]
 
       # get the main reading frame
-      main_rf = frames_histo.map { |_k, v| v }.max
-      @prediction.nucleotide_rf = frames_histo.select { |_k, v| v == main_rf }.first.first
+      main_rf = frames.map { |_k, v| v }.max
+      @prediction.nucleotide_rf = frames.select { |_k, v| v == main_rf }.first.first
 
       @validation_report = BlastRFValidationOutput.new(@short_header, @header,
-                                                       @description,
-                                                       frames_histo)
-      @validation_report.running_time = Time.now - start
+                                                       @description, frames)
+      @validation_report.run_time = Time.now - start
       @validation_report
 
     rescue NotEnoughHitsError
       @validation_report =  ValidationReport.new('Not enough evidence',
                                                  :warning, @short_header,
-                                                 @header, @description,
-                                                 @approach, @explanation,
-                                                 @conclusion)
+                                                 @header, @description)
     rescue Exception
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
-                                                @description, @approach,
-                                                @explanation, @conclusion)
+                                                @description)
       @validation_report.errors.push 'Unexpected Error'
     end
   end

data/lib/genevalidator/validation_duplication.rb

@@ -1,6 +1,12 @@
-require 'genevalidator/validation_report'
+require 'bio'
+require 'forwardable'
+require 'statsample'
+
 require 'genevalidator/exceptions'
 require 'genevalidator/ext/array'
+require 'genevalidator/validation_report'
+require 'genevalidator/validation_test'
+
 module GeneValidator
   ##
   # Class that stores the validation output information
@@ -71,12 +77,14 @@ module GeneValidator
   # This class contains the methods necessary for
   # finding duplicated subsequences in the predicted gene
   class DuplicationValidation < ValidationTest
+    extend Forwardable
+    def_delegators GeneValidator, :opt, :config
+
     attr_reader :raw_seq_file
     attr_reader :index_file_name
     attr_reader :raw_seq_file_load
 
-    def initialize(type, prediction, hits, raw_seq_file, index_file_name,
-                   raw_seq_file_load, db, num_threads)
+    def initialize(prediction, hits)
       super
       @short_header      = 'Duplication'
       @header            = 'Duplication'
@@ -84,11 +92,12 @@ module GeneValidator
                            ' in the predicted gene by counting the hsp' \
                            ' residue coverage of the prediction, for each hit.'
       @cli_name          = 'dup'
-      @raw_seq_file      = raw_seq_file
-      @index_file_name   = index_file_name
-      @raw_seq_file_load = raw_seq_file_load
-      @db                = db
-      @num_threads       = num_threads
+      @raw_seq_file      = opt[:raw_sequences]
+      @index_file_name   = config[:raw_seq_file_index]
+      @raw_seq_file_load = config[:raw_seq_file_load]
+      @db                = opt[:db]
+      @num_threads       = opt[:num_threads]
+      @type              = config[:type]
     end
 
     def in_range?(ranges, idx)
@@ -214,7 +223,7 @@ module GeneValidator
                                                              @header,
                                                              @description, 1,
                                                              averages)
-        @validation_report.running_time = Time.now - start
+        @validation_report.run_time = Time.now - start
         return @validation_report
       end
 
@@ -224,31 +233,27 @@ module GeneValidator
                                                            @header,
                                                            @description, pval,
                                                            averages)
-      @running_time = Time.now - start
+      @run_time = Time.now - start
       @validation_report
 
     rescue NotEnoughHitsError
       @validation_report = ValidationReport.new('Not enough evidence', :warning,
                                                 @short_header, @header,
-                                                @description, @explanation,
-                                                @conclusion)
+                                                @description)
     rescue NoMafftInstallationError
       @validation_report = ValidationReport.new('Mafft error', :error,
                                                 @short_header, @header,
-                                                @description, @explanation,
-                                                @conclusion)
+                                                @description)
       @validation_report.errors.push NoMafftInstallationError
     rescue NoInternetError
       @validation_report = ValidationReport.new('Internet error', :error,
                                                 @short_header, @header,
-                                                @description, @explanation,
-                                                @conclusion)
+                                                @description)
       @validation_report.errors.push NoInternetError
     rescue Exception
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
-                                                @description, @explanation,
-                                                @conclusion)
+                                                @description)
       @validation_report.errors.push 'Unexpected Error'
     end
 
@@ -256,7 +261,6 @@ module GeneValidator
     # wilcox test implementation from statsample ruby gem
     # many thanks to Claudio for helping us with the implementation!
     def wilcox_test(averages)
-      require 'statsample'
       wilcox = Statsample::Test.wilcoxon_signed_rank(averages.to_scale,
                                                      Array.new(averages.length,
                                                                1).to_scale)

data/lib/genevalidator/validation_gene_merge.rb

@@ -1,6 +1,11 @@
-require 'json'
-require 'genevalidator/validation_report'
+require 'forwardable'
+require 'statsample'
+
+require 'genevalidator/exceptions'
 require 'genevalidator/ext/array'
+require 'genevalidator/validation_report'
+require 'genevalidator/validation_test'
+
 module GeneValidator
   ##
   # Class that stores the validation output information
@@ -83,26 +88,23 @@ module GeneValidator
   # checking whether there is evidence that the
   # prediction is a merge of multiple genes
   class GeneMergeValidation < ValidationTest
-    attr_reader :hits
     attr_reader :prediction
-    attr_reader :filename
+    attr_reader :hits
 
     ##
     # Initilizes the object
     # Params:
-    # +type+: type of the predicted sequence (:nucleotide or :protein)
     # +prediction+: a +Sequence+ object representing the blast query
     # +hits+: a vector of +Sequence+ objects (representing blast hits)
-    # +filename+: name of the input file, used when generatig the plot files
+    # +plot_path+: name of the input file, used when generatig the plot files
     # +boundary+: the offset of the hit from which we start analysing the hit
-    def initialize(type, prediction, hits, filename, boundary = 10)
+    def initialize(prediction, hits, boundary = 10)
       super
-      @short_header = 'Gene_Merge'
+      @short_header = 'GeneMerge'
       @header       = 'Gene Merge'
       @description  = 'Check whether BLAST hits make evidence about a merge' \
                       ' of two genes that match the predicted gene.'
       @cli_name     = 'merge'
-      @filename     = filename
       @boundary     = boundary
     end
 
@@ -158,14 +160,18 @@ module GeneValidator
       @validation_report.plot_files.push(plot1)
       plot2 = plot_matched_regions
       @validation_report.plot_files.push(plot2)
-      @validation_report.running_time = Time.now - start
+      @validation_report.run_time = Time.now - start
       @validation_report
 
     rescue NotEnoughHitsError
       @validation_report = ValidationReport.new('Not enough evidence', :warning,
                                                 @short_header, @header,
-                                                @description, @approach,
-                                                @explanation, @conclusion)
+                                                @description)
+    rescue Exception
+      @validation_report = ValidationReport.new('Unexpected error', :error,
+                                                @short_header, @header,
+                                                @description)
+      @validation_report.errors.push 'Unexpected Error'
     end
 
     ##
@@ -175,29 +181,25 @@ module GeneValidator
     # +output+: location where the plot will be saved in jped file format
     # +hits+: array of Sequence objects
     # +prediction+: Sequence objects
-    def plot_matched_regions(output = "#{filename}_match.json", hits = @hits)
-
-      colors   = ['orange', 'blue']  ##{colors[i%2]
-      f        = File.open(output, 'w')
+    def plot_matched_regions(hits = @hits)
       no_lines = hits.length
 
       hits_less = hits[0..[no_lines, hits.length - 1].min]
 
-      f.write((hits_less.each_with_index.map { |hit, i|
+      data = hits_less.each_with_index.map { |hit, i|
         { 'y' => i,
           'start' => hit.hsp_list.map(&:match_query_from).min,
           'stop' => hit.hsp_list.map(&:match_query_to).max,
-          'color'=>'black',
-          'dotted'=>'true'}}.flatten +
+          'color' =>'black',
+          'dotted' =>'true'}}.flatten +
         hits_less.each_with_index.map { |hit, i|
           hit.hsp_list.map { |hsp|
             { 'y' => i,
               'start' => hsp.match_query_from,
               'stop' => hsp.match_query_to,
-              'color' => 'orange'} } }.flatten).to_json)
-      f.close
+              'color' => 'orange'} } }.flatten
 
-      Plot.new(output.scan(%r{([^/]+)$})[0][0],
+      Plot.new(data,
                :lines,
                'Gene Merge Validation: Query coord covered by blast hit (1 line/hit)',
                '',
@@ -214,60 +216,24 @@ module GeneValidator
     # +y_intercept+: the ecuation of the line is y= slope*x + y_intercept
     # +output+: location where the plot will be saved in jped file format
     # +hits+: array of Sequence objects
-    def plot_2d_start_from(slope = nil, y_intercept = nil,
-                           output = "#{filename}_match_2d.json", hits = @hits)
+    def plot_2d_start_from(slope = nil, y_intercept = nil, hits = @hits)
       pairs = hits.map do |hit|
         Pair.new(hit.hsp_list.map(&:match_query_from).min,
                  hit.hsp_list.map(&:match_query_to).max)
       end
 
-      xx = pairs.map(&:x)
-      yy = pairs.map(&:y)
-
-      freq_x = xx.inject(Hash.new(0)) { |h, v| h[v] += 1; h }
-      filename_x = "#{filename}_merge_x.json"
-      f = File.open(filename_x, 'w')
-      f.write([freq_x.collect { |k,v|
-          { 'key' => k, 'value' => v, 'main' => (1==2) }
-        }].to_json)
-      f.close
-      plot3 = Plot.new(filename_x.scan(%r{([^/]+)$})[0][0],
-                       :simplebars,
-                       '[Gene Merge] X projection',
-                       '',
-                       'x projection',
-                       'number of sequences')
-#       @validation_report.plot_files.push(plot3)
-
-      freq_y = yy.inject(Hash.new(0)) { |h,v| h[v] += 1; h }
-      filename_y = "#{filename}_merge_y.json"
-      f = File.open(filename_y, 'w')
-      f.write([freq_y.collect { |k, v|
-          { 'key' => k, 'value' => v, 'main' => (1 == 2) }
-        }].to_json)
-      f.close
-      plot4 = Plot.new(filename_y.scan(%r{([^/]+)$})[0][0],
-                       :simplebars,
-                       '[Gene Merge] Y projection',
-                       '',
-                       'y projection',
-                       'number of sequences')
-#       @validation_report.plot_files.push(plot4)
-
-      f = File.open(output, 'w')
-      f.write(hits.map { |hit| {'x' => hit.hsp_list.map(&:match_query_from).min,
+      data = hits.map { |hit| { 'x' => hit.hsp_list.map(&:match_query_from).min,
                                 'y' => hit.hsp_list.map(&:match_query_to).max,
-                                'color' => 'red'}}.to_json)
-      f.close
+                                'color' => 'red'}}
 
-      Plot.new(output.scan(%r{([^/]+)$})[0][0],
+      Plot.new(data,
                :scatter,
                'Gene Merge Validation: Start/end of matching hit coord. on query (1 point/hit)',
                '',
                'Start Offset (most left hsp)',
                'End Offset (most right hsp)',
-               y_intercept,
-               slope)
+               y_intercept.to_s,
+               slope.to_s)
     end
 
     ##
@@ -314,7 +280,6 @@ module GeneValidator
     # Output:
     # The ecuation of the regression line: [y slope]
     def slope_statsample(xx, yy)
-      require 'statsample'
       sr = Statsample::Regression.simple(xx.to_scale, yy.to_scale)
       [sr.a, sr.b]
     end

data/lib/genevalidator/validation_length_cluster.rb

@@ -1,8 +1,10 @@
-require 'json'
+require 'forwardable'
+
 require 'genevalidator/clusterization'
+require 'genevalidator/exceptions'
 require 'genevalidator/validation_report'
 require 'genevalidator/validation_test'
-require 'genevalidator/exceptions'
+
 module GeneValidator
   ##
   # Class that stores the validation output information
@@ -65,7 +67,6 @@ module GeneValidator
   # This class contains the methods necessary for
   # length validation by hit length clusterization
   class LengthClusterValidation < ValidationTest
-    attr_reader :filename
     attr_reader :clusters
     attr_reader :max_density_cluster
 
@@ -76,9 +77,8 @@ module GeneValidator
     # +prediction+: a +Sequence+ object representing the blast query
     # +hits+: a vector of +Sequence+ objects (representing blast hits)
     # +dilename+: +String+ with the name of the fasta file
-    def initialize(type, prediction, hits, filename)
+    def initialize(prediction, hits)
       super
-      @filename     = filename
       @short_header = 'LengthCluster'
       @header       = 'Length Cluster'
       @description  = 'Check whether the prediction length fits most of the' \
@@ -117,20 +117,18 @@ module GeneValidator
       plot1 = plot_histo_clusters
       @validation_report.plot_files.push(plot1)
 
-      @validation_report.running_time = Time.now - start
+      @validation_report.run_time = Time.now - start
 
       @validation_report
 
     rescue NotEnoughHitsError
       @validation_report = ValidationReport.new('Not enough evidence', :warning,
                                                 @short_header, @header,
-                                                @description, @approach,
-                                                @explanation, @conclusion)
+                                                @description)
     rescue Exception
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
-                                                @description, @approach,
-                                                @explanation, @conclusion)
+                                                @description)
       @validation_report.errors.push 'Unexpected Error'
     end
 
@@ -175,25 +173,24 @@ module GeneValidator
     ##
     # Generates a json file containing data used for plotting the histogram
     # of the length distribution given a lust of Cluster objects
-    # +output+: filename where to save the graph
+    # +output+: plot_path where to save the graph
     # +clusters+: array of +Cluster+ objects
     # +max_density_cluster+: index of the most dense cluster
     # +prediction+: +Sequence+ object
     # Output:
     # +Plot+ object
-    def plot_histo_clusters(output = "#{@filename}_len_clusters.json",
+    def plot_histo_clusters(output = "#{@plot_path}_len_clusters.json",
                           clusters = @clusters,
                           max_density_cluster = @max_density_cluster,
                           prediction = @prediction)
 
-      f = File.open(output, 'w')
-      f.write(clusters.each_with_index.map { |cluster, i|
+      data = clusters.each_with_index.map { |cluster, i|
         cluster.lengths.collect { |k, v|
           { 'key' => k, 'value' => v, 'main' => (i == max_density_cluster) }
         }
-      }.to_json)
-      f.close
-      Plot.new(output.scan(%r{([^/]+)$})[0][0],
+      }
+
+      Plot.new(data,
                :bars,
                'Length Cluster Validation: Distribution of BLAST hit lengths',
                'Query Sequence, black;Most Dense Cluster,red;Other Hits, blue',
@@ -201,41 +198,5 @@ module GeneValidator
                'Number of Sequences',
                prediction.length_protein)
     end
-
-    ##
-    # Generates a json file cotaining data used for plotting
-    # lines corresponding to the start and end hit offsets
-    # Params:
-    # +output+: filename where to save the graph
-    # +hits+: array of Sequence objects
-    # Output:
-    # +Plot+ object
-    def plot_len_clusters(output = "#{@filename}_len.json", _hits = @hits)
-      f = File.open(output, 'w')
-      lst = @hits.sort { |a, b| a.length_protein <=> b.length_protein }
-
-      no_lines = 100
-
-      lst_less = lst[0..[no_lines, lst.length - 1].min]
-
-      f.write((lst_less.each_with_index.map { |hit, i|
-        { 'y' => i, 'start' => 0, 'stop' => hit.length_protein,
-          'color' => 'gray' }
-      } + lst_less.each_with_index.map { |hit, i|
-        hit.hsp_list.map { |hsp|
-          { 'y' => i, 'start' => hsp.hit_from, 'stop' => hsp.hit_to,
-            'color' => 'red' }
-        }
-      }.flatten).to_json)
-
-      f.close
-      Plot.new(output.scan(%r{([^/]+)$})[0][0],
-               :lines,
-               '[Length Cluster] Matched regions in hits',
-               'hit, gray;high-scoring segment pairs (hsp), red',
-               'offset in the hit',
-               'number of the hit',
-               lst_less.length)
-    end
   end
 end