genevalidator 1.6.2 → 1.6.3

data/lib/genevalidator/pool.rb

@@ -4,7 +4,7 @@
 # Copyright © 2012, Kim Burgestrand kim@burgestrand.se
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the “Software”), to deal
+# of this software and associated documentation files (the "Software"), to deal
 # in the Software without restriction, including without limitation the rights
 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 # copies of the Software, and to permit persons to whom the Software is
@@ -13,7 +13,7 @@
 # The above copyright notice and this permission notice shall be included in
 # all copies or substantial portions of the Software.
 #
-# THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
@@ -23,6 +23,7 @@
 
 require 'thread'
 
+# Class that creates a thread safe pool.
 class Pool
   def initialize(size)
     @size = size
@@ -52,13 +53,13 @@ class Pool
   end
 end
 
-if $0 == __FILE__
+if $PROGRAM_NAME == __FILE__
   p = Pool.new(10)
 
   20.times do |i|
     p.schedule do
       sleep rand(4) + 2
-      $stderr.puts "Job #{i} finished by thread #{Thread.current[:id]}"
+      $stderr.puts "Job #{i} finished by thread #{Thread.current[:id]}\n"
     end
   end
   at_exit { p.shutdown }

data/lib/genevalidator/query.rb

@@ -0,0 +1,37 @@
+module GeneValidator
+  # This is a class for the storing data on each sequence
+  class Query
+    attr_accessor :type # protein | mRNA
+    attr_accessor :definition
+    attr_accessor :identifier
+    attr_accessor :species
+    attr_accessor :accession_no
+    attr_accessor :length_protein
+    attr_accessor :reading_frame
+    attr_accessor :hsp_list # array of Hsp objects
+
+    attr_accessor :raw_sequence
+    attr_accessor :protein_translation # used only for nucleotides
+    attr_accessor :nucleotide_rf # used only for nucleotides
+
+    def initialize
+      @hsp_list            = []
+      @raw_sequence        = nil
+      @protein_translation = nil
+      @nucleotide_rf       = nil
+    end
+
+    def protein_translation
+      (@type == :protein) ? raw_sequence : @protein_translation
+    end
+
+    ##
+    # Initializes the corresponding attribute of the sequence
+    # with respect to the column name of the tabular blast output
+    def init_tabular_attribute(hash)
+      @identifier     = hash['sseqid'] if hash['sseqid']
+      @accession_no   = hash['sacc'] if hash['sacc']
+      @length_protein = hash['slen'].to_i if hash['slen']
+    end
+  end
+end

data/lib/genevalidator/tabular_parser.rb

@@ -1,9 +1,9 @@
 require 'csv'
 require 'forwardable'
 
-require 'genevalidator/sequences'
-require 'genevalidator/hsp'
 require 'genevalidator/exceptions'
+require 'genevalidator/hsp'
+require 'genevalidator/query'
 
 #
 module GeneValidator
@@ -52,7 +52,6 @@ module GeneValidator
         @rows.next
         break unless entry == current_entry
       end
-      # rescue StopIteration
     end
 
     alias move_to_next_query next
@@ -79,7 +78,7 @@ module GeneValidator
       grouped_hits = hits.group_by { |row| row['sseqid'] }
 
       grouped_hits.each do |query_id, row|
-        hit_seq = Sequence.new
+        hit_seq = Query.new
         hit_seq.init_tabular_attribute(row[0])
 
         initialise_all_hsps(query_id, hits, hit_seq)

data/lib/genevalidator/validation.rb

@@ -4,7 +4,7 @@ require 'genevalidator/blast'
 require 'genevalidator/exceptions'
 require 'genevalidator/output'
 require 'genevalidator/pool'
-require 'genevalidator/sequences'
+require 'genevalidator/query'
 require 'genevalidator/validation_length_cluster'
 require 'genevalidator/validation_length_rank'
 require 'genevalidator/validation_blast_reading_frame'
@@ -17,7 +17,7 @@ require 'genevalidator/validation_alignment'
 module GeneValidator
   Pair1 = Struct.new(:x, :y)
 
-  # Class that initalises separate Validate.new() instances for each query.
+  # Class that initalises a separate Validate.new() instance for each query.
   class Validations
     extend Forwardable
     def_delegators GeneValidator, :opt, :config, :query_idx
@@ -64,7 +64,7 @@ module GeneValidator
       query        = IO.binread(input_file, start_offset, end_offset)
       parse_query  = query.scan(/>([^\n]*)\n([A-Za-z\n]*)/)[0]
 
-      prediction                = Sequence.new
+      prediction                = Query.new
       prediction.definition     = parse_query[0].gsub("\n", '')
       prediction.identifier     = prediction.definition.gsub(/ .*/, '')
       prediction.type           = seq_type
@@ -87,7 +87,8 @@ module GeneValidator
   # Class that runs the validations (Instatiated for each query)
   class Validate
     extend Forwardable
-    def_delegators GeneValidator, :opt, :config, :mutex_array, :overview
+    def_delegators GeneValidator, :opt, :config, :mutex_array, :overview,
+                   :query_idx
 
     ##
     # Initilizes the object
@@ -102,8 +103,8 @@ module GeneValidator
       @config      = config
       @mutex_array = mutex_array
       @run_output  = nil
-
       @overview    = overview
+      @query_idx   = query_idx
     end
 
     ##
@@ -200,14 +201,18 @@ module GeneValidator
     def compute_scores
       validations        = @run_output.validations
       scores             = {}
-      scores[:successes] = validations.map { |v| v.result == v.expected }.count(true)
-      scores[:fails] = validations.map { |v| v.validation != :unapplicable && v.validation != :error && v.result != v.expected }.count(true)
+      scores[:successes] = validations.count { |v| v.result == v.expected }
+      scores[:fails] = validations.count { |v| v.validation != :unapplicable && v.validation != :error && v.result != v.expected }
       scores         = length_validation_scores(validations, scores)
 
       @run_output.successes     = scores[:successes]
       @run_output.fails         = scores[:fails]
-      total_query              = scores[:successes].to_i + scores[:fails]
-      @run_output.overall_score = (scores[:successes] * 100 / total_query).round
+      total_query               = scores[:successes].to_i + scores[:fails]
+      if total_query == 0
+        @run_output.overall_score = 0
+      else
+        @run_output.overall_score = (scores[:successes] * 90 / total_query).round
+      end
     end
 
     # Since there are two length validations, it is necessary to adjust the
@@ -244,8 +249,8 @@ module GeneValidator
       errors      = []
       vals.each do |v|
         unless v.errors.nil?
-          no_mafft += v.errors.select { |e| e == NoMafftInstallationError }.length
-          no_internet += v.errors.select { |e| e == NoInternetError }.length
+          no_mafft += v.errors.count { |e| e == NoMafftInstallationError }
+          no_internet += v.errors.count { |e| e == NoInternetError }
         end
         errors.push(v.short_header) if v.validation == :error
       end

data/lib/genevalidator/validation_alignment.rb

@@ -2,6 +2,7 @@ require 'bio'
 require 'forwardable'
 
 require 'genevalidator/exceptions'
+require 'genevalidator/get_raw_sequences'
 require 'genevalidator/validation_report'
 require 'genevalidator/validation_test'
 
@@ -126,8 +127,8 @@ module GeneValidator
       n = 50 if n > 50
 
       fail NotEnoughHitsError unless hits.length >= n
-      fail Exception unless prediction.is_a?(Sequence) &&
-                            hits[0].is_a?(Sequence)
+      fail unless prediction.is_a?(Query) && hits[0].is_a?(Query)
+
       start = Time.new
       # get the first n hits
       less_hits    = @hits[0..[n - 1, @hits.length].min]
@@ -135,19 +136,10 @@ module GeneValidator
 
       # get raw sequences for less_hits
       less_hits.map do |hit|
-        # get gene by accession number
         next unless hit.raw_sequence.nil?
-
-        hit.get_sequence_from_index_file(@raw_seq_file, @index_file_name,
-                                         hit.identifier, @raw_seq_file_load)
-
-        if hit.raw_sequence.nil? || hit.raw_sequence.empty?
-          seq_type = (hit.type == :protein) ? 'protein' : 'nucleotide'
-          hit.get_sequence_by_accession_no(hit.accession_no, seq_type, @db)
-        end
-
+        hit.raw_sequence = FetchRawSequences.run(hit.identifier,
+                                                 hit.accession_no)
         useless_hits.push(hit) if hit.raw_sequence.nil?
-        useless_hits.push(hit) if hit.raw_sequence.empty?
       end
 
       useless_hits.each { |hit| less_hits.delete(hit) }
@@ -210,7 +202,7 @@ module GeneValidator
                                                 :error, @short_header,
                                                 @header, @description)
       @validation_report.errors.push 'Multiple reading frames Error'
-    rescue Exception
+    rescue
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
                                                 @description)
@@ -230,7 +222,7 @@ module GeneValidator
     # Array of +String+s, corresponding to the multiple aligned sequences
     # the prediction is the last sequence in the vector
     def multiple_align_mafft(prediction = @prediction, hits = @hits)
-      fail Exception unless prediction.is_a?(Sequence) && hits[0].is_a?(Sequence)
+      fail unless prediction.is_a?(Query) && hits[0].is_a?(Query)
 
       options = ['--maxiterate', '1000', '--localpair', '--anysymbol',
                  '--quiet', '--thread', "#{@num_threads}"]
@@ -247,7 +239,7 @@ module GeneValidator
       end
 
       @multiple_alignment
-    rescue Exception
+    rescue
       raise NoMafftInstallationError
     end
 
@@ -319,7 +311,7 @@ module GeneValidator
       return 1 if no_conserved_residues == 0
 
       # no of conserved residues from the hita that appear in the prediction
-      no_conserved_pred = consensus.split(//).each_index.select { |j| consensus[j] != '-' && consensus[j] != '?' && consensus[j] == prediction_raw[j] }.length
+      no_conserved_pred = consensus.split(//).each_index.count { |j| consensus[j] != '-' && consensus[j] != '?' && consensus[j] == prediction_raw[j] }
 
       no_conserved_pred / (no_conserved_residues + 0.0)
     end
@@ -333,7 +325,8 @@ module GeneValidator
     # +threshold+: percentage of genes that are considered in statistical model
     # Output:
     # +String+ representing the statistical model
-    # +Array+ with the maximum frequeny of the majoritary residue for each position
+    # +Array+ with the maximum frequeny of the majoritary residue for each
+    # position
     def get_sm_pssm(ma = @multiple_alignment, threshold = 0.7)
       sm = ''
       freq = []
@@ -442,19 +435,20 @@ module GeneValidator
       # plot consensus
       consensus_all_ranges.map { |range| { 'y' => 0, 'start' => range.first, 'stop' => range.last, 'color' => 'yellow', 'height' => -1 } }.flatten
 
-      yAxisValues = 'Prediction'
-      (1..ma.length - 1).each { |i| yAxisValues << ", hit #{i}" }
+      y_axis_values = 'Prediction'
+      (1..ma.length - 1).each { |i| y_axis_values << ", hit #{i}" }
 
-      yAxisValues << ', Statistical Model'
+      y_axis_values << ', Statistical Model'
 
       Plot.new(data,
                :align,
-               'Missing/Extra sequences Validation: Multiple Align. & Statistical model of hits',
+               'Missing/Extra sequences Validation: Multiple Align. &' \
+               'Statistical model of hits',
                'Conserved Region, Yellow',
                'Offset in the Alignment',
                '',
                ma.length + 1,
-               yAxisValues)
+               y_axis_values)
     end
   end
 end

data/lib/genevalidator/validation_blast_reading_frame.rb

@@ -101,7 +101,7 @@ module GeneValidator
       end
 
       fail NotEnoughHitsError unless hits.length >= 5
-      fail Exception unless prediction.is_a?(Sequence) && hits[0].is_a?(Sequence)
+      fail unless prediction.is_a?(Query) && hits[0].is_a?(Query)
 
       start = Time.now
 
@@ -110,7 +110,7 @@ module GeneValidator
 
       # get the main reading frame
       main_rf = frames.map { |_k, v| v }.max
-      @prediction.nucleotide_rf = frames.select { |_k, v| v == main_rf }.first.first
+      @prediction.nucleotide_rf = frames.find { |_k, v| v == main_rf }.first
 
       @validation_report = BlastRFValidationOutput.new(@short_header, @header,
                                                        @description, frames)
@@ -121,7 +121,7 @@ module GeneValidator
       @validation_report =  ValidationReport.new('Not enough evidence',
                                                  :warning, @short_header,
                                                  @header, @description)
-    rescue Exception
+    rescue
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
                                                 @description)

data/lib/genevalidator/validation_duplication.rb

@@ -4,6 +4,7 @@ require 'statsample'
 
 require 'genevalidator/exceptions'
 require 'genevalidator/ext/array'
+require 'genevalidator/get_raw_sequences'
 require 'genevalidator/validation_report'
 require 'genevalidator/validation_test'
 
@@ -113,35 +114,24 @@ module GeneValidator
     # +DuplicationValidationOutput+ object
     def run(n = 10)
       fail NotEnoughHitsError unless hits.length >= 5
-      fail Exception unless prediction.is_a?(Sequence) &&
-                            !prediction.raw_sequence.nil? &&
-                            hits[0].is_a?(Sequence)
+      fail unless prediction.is_a?(Query) && !prediction.raw_sequence.nil? &&
+                  hits[0].is_a?(Query)
 
       start = Time.new
       # get the first n hits
       less_hits = @hits[0..[n - 1, @hits.length].min]
       useless_hits = []
-
       # get raw sequences for less_hits
       less_hits.map do |hit|
-        # get gene by accession number
         next unless hit.raw_sequence.nil?
-
-        hit.get_sequence_from_index_file(@raw_seq_file, @index_file_name,
-                                         hit.identifier, @raw_seq_file_load)
-
-        if hit.raw_sequence.nil? || hit.raw_sequence.empty?
-          seq_type = (hit.type == :protein) ? 'protein' : 'nucleotide'
-          hit.get_sequence_by_accession_no(hit.accession_no, seq_type, @db)
-        end
-
+        hit.raw_sequence = FetchRawSequences.run(hit.identifier,
+                                                 hit.accession_no)
         useless_hits.push(hit) if hit.raw_sequence.nil?
-        useless_hits.push(hit) if hit.raw_sequence.empty?
       end
 
       useless_hits.each { |hit| less_hits.delete(hit) }
 
-      fail NoInternetError if less_hits.length.nil?
+      fail NoInternetError if less_hits.length == 0
 
       averages = []
 
@@ -185,7 +175,7 @@ module GeneValidator
               raw_align.each { |seq| align.push(seq.to_s) }
               hit_alignment   = align[0]
               query_alignment = align[1]
-            rescue Exception
+            rescue
               raise NoMafftInstallationError
             end
           end
@@ -250,7 +240,7 @@ module GeneValidator
                                                 @short_header, @header,
                                                 @description)
       @validation_report.errors.push NoInternetError
-    rescue Exception
+    rescue
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
                                                 @description)

data/lib/genevalidator/validation_gene_merge.rb

@@ -114,7 +114,7 @@ module GeneValidator
     # +GeneMergeValidationOutput+ object
     def run
       fail NotEnoughHitsError unless hits.length >= 5
-      fail Exception unless prediction.is_a?(Sequence) && hits[0].is_a?(Sequence)
+      fail unless prediction.is_a?(Query) && hits[0].is_a?(Query)
 
       start = Time.now
 
@@ -135,7 +135,7 @@ module GeneValidator
         end
       end
 
-      line_slope = slope(xx, yy, (1..hits.length).map{ |x| 1 / (x + 0.0) })
+      line_slope = slope(xx, yy, (1..hits.length).map { |x| 1 / (x + 0.0) })
       ## YW - what is this weighting?
 
       unimodality = false
@@ -167,7 +167,7 @@ module GeneValidator
       @validation_report = ValidationReport.new('Not enough evidence', :warning,
                                                 @short_header, @header,
                                                 @description)
-    rescue Exception
+    rescue
       @validation_report = ValidationReport.new('Unexpected error', :error,
                                                 @short_header, @header,
                                                 @description)
@@ -190,18 +190,19 @@ module GeneValidator
         { '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
+              'color' => 'orange' } } }.flatten
 
       Plot.new(data,
                :lines,
-               'Gene Merge Validation: Query coord covered by blast hit (1 line/hit)',
+               'Gene Merge Validation: Query coord covered by blast hit' \
+               ' (1 line/hit)',
                '',
                'Offset in Prediction',
                'Hit Number',
@@ -224,11 +225,12 @@ module GeneValidator
 
       data = hits.map { |hit| { 'x' => hit.hsp_list.map(&:match_query_from).min,
                                 'y' => hit.hsp_list.map(&:match_query_to).max,
-                                'color' => 'red'}}
+                                'color' => 'red' } }
 
       Plot.new(data,
                :scatter,
-               'Gene Merge Validation: Start/end of matching hit coord. on query (1 point/hit)',
+               'Gene Merge Validation: Start/end of matching hit coord. on' \
+               ' query (1 point/hit)',
                '',
                'Start Offset (most left hsp)',
                'End Offset (most right hsp)',