genevalidator 1.6.5 → 1.6.6

checksums.yaml

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r=t[e];GV.addPlot(r.data,a,r.type,r.title,r.footer,r.xtitle,r.ytitle,r.aux1,r.aux2)}},GV.addExplanation=function(t,a){var e="#row"+t,r="<p><b>Approach:</b> "+a.approach+"</p>",n="<p><b>Explanation:</b> "+a.explanation+"</p>",o="<p><b>Conclusion:</b> "+a.conclusion+"</p>",l=$('<div id="'+t+'explanation" class="alert alert-info explanation_alert" role="alert">'+r+n+o+"</div>");$(e).prepend(l)},GV.addPlot=function(t,a,e,r,n,o,l,s,i){var c;switch(c=""===n?[]:n.split(";"),e){case"scatter":GV.plot_scatter(t,a,r,n,o,l,s,i);break;case"bars":GV.plot_bars(t,a,r,c,o,l,s);break;case"simplebars":GV.plot_simple_bars(t,a,r,c,o,l);break;case"lines":null!==i&&(i=i.split(",")),GV.plot_lines(t,a,r,c,o,l,s,i);break;case"align":null!==i&&(i=i.split(",")),GV.plot_align(t,a,r,c,o,l,s,i)}},GV.color_beautification=function(t){switch(t){case"red":return d3.rgb(189,54,47);case"blue":return d3.rgb(58,135,173);case"green":return d3.rgb(70,136,71);case"yellow":return d3.rgb(255,255,51);case"orange":return d3.rgb(248,148,6);case"violet":return d3.rgb(153,0,153);case"gray":return d3.rgb(160,160,160);default:return t}},GV.plot_bars=function(t,a,e,r,n,o,l){var s={top:70,right:50,bottom:75,left:50},i=600-s.left-s.right,c=500-s.top-s.bottom,d=d3.select("#".concat(a)).append("svg").attr("width",i+s.left+s.right).attr("height",c+s.top+s.bottom).append("g").attr("transform","translate("+s.left+","+s.top+")");d.append("text").attr("x",i/2).attr("y",-45).attr("text-anchor","middle").style("font-size","16px").text(e);var p=100,u=[].concat.apply([],t),f=d3.max(u,function(t){return t.value})+3,h=d3.scale.linear().domain([0,f+f/10]).range([c,0]),x=d3.min(u,function(t){return t.key});void 0!==l&&(x=Math.min(x,l));var g=d3.max(u,function(t){return t.key});void 0!==l&&(g=Math.max(g,l));var m=d3.scale.linear().domain([x-p,g+p]).range([13,i]),v=d3.svg.axis().scale(m).orient("bottom").ticks(8),y=d3.svg.axis().scale(h).orient("left").tickFormat(d3.format("d")).ticks(8);d.append("g").attr("class","x axis").attr("transform","translate(0,"+c+")").call(v).append("text").attr("class","label").attr("x",(i-n.length)/2-50).attr("y",35).style("text-anchor","start").text(n),d.append("g").attr("class","y axis").call(y).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(c+o.length)/2-50).attr("y",-40).style("text-anchor","start").text(o),t.map(function(t){d.selectAll(".bar").data(t).enter().append("rect").attr("x",function(t){return m(t.key)}).attr("width",6).attr("y",function(t){return h(t.value)}).attr("height",function(t){return c-h(t.value)}).attr("fill",function(t){return t.main===!0?GV.color_beautification("red"):GV.color_beautification("blue")})}),void 0!==l&&(d.append("rect").attr("x",m(l)).attr("width",4).attr("y",h(f+f/10)).style("opacity",.6).attr("height",c-h(f+f/8)).attr("fill",GV.color_beautification("black")),d.append("text").attr("transform","rotate(-90)").attr("x",-f/10-35).attr("y",m(l)-5).text("query"));for(var b=0,w=0,G=0;G<r.length;G++){var 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t.key}),g=d3.scale.linear().domain([h-d,x+d]).range([13,s]),m=d3.svg.axis().scale(g).orient("bottom").ticks(8),v=d3.svg.axis().scale(f).orient("left").tickFormat(d3.format("d")).ticks(8);c.append("g").attr("class","x axis").attr("transform","translate(0,"+i+")").call(m).append("text").attr("class","label").attr("x",(s-n.length)/2-50).attr("y",35).style("text-anchor","start").text(n),c.append("g").attr("class","y axis").call(v).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(i+o.length)/2-50).attr("y",-40).style("text-anchor","start").text(o),t.map(function(t){c.selectAll(".bar").data(t).enter().append("rect").attr("x",function(t){return g(t.key)}).attr("width",6).attr("y",function(t){return f(t.value)}).attr("height",function(t){return i-f(t.value)}).attr("fill",function(t){return t.main===!0?GV.color_beautification("red"):GV.color_beautification("blue")})})},GV.plot_scatter=function(t,a,e,r,n,o,l,s){var 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g+=1,s[g]})).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(d+o.length)/2-50).attr("y",-40).style("text-anchor","start").text(o):x.append("g").attr("class","y axis").call(h).append("text").attr("class","label").attr("transform","rotate(-90)").attr("x",-(d+o.length)/2-50).attr("y",-40).style("text-anchor","start").text(o),x.selectAll(".dot").data(t).enter().append("line").attr("x1",function(t){return p(t.start)}).attr("y1",function(t){return u(t.y)}).attr("x2",function(t){return p(t.stop)}).attr("y2",function(t){return u(t.y)}).attr("stroke-width",function(t){return-1==t.height?d/l:d/l*t.height}).attr("stroke",function(t){return GV.color_beautification(t.color)});for(var m=0,v=0,y=0;y<r.length;y++){var b=r[y].split(",");v=v+8*b[0].length+15}for(var w=0;w<r.length;w++){var G=r[w].split(",");x.append("rect").attr("x",(c-v)/2+m).attr("y",-30).attr("width",10).attr("height",10).style("fill",GV.color_beautification(G[1].replace(/\s+/g,""))),x.append("text").attr("x",(c-v)/2+m+15).attr("y",-20).text(G[0]),m=m+8*G[0].length+15}}}();
 // Script.js
 function initTableSorter(){$.tablesorter.addParser({id:"star_scores",is:function(){return!1},format:function(t,e,r,a){var s=$(r);return 1===a?s.attr("data-score")||t:t},parsed:!1,type:"numeric"}),$("table").tablesorter({headers:{1:{sorter:"star_scores"}},sortList:[[0,0]]})}$(document).ready(function(){window.chrome&&"file:"===window.location.protocol&&($("#mainbrowseralertText").text("Some features are not supported in this browser and have been disabled."),$("#browseralert").modal()),GV.toggleOverviewBtn(),initTableSorter(),$("[data-toggle='tooltip']").tooltip()}),$(document).on("click","td, .plot_btn",function(t){if($(this).hasClass("success")||$(this).hasClass("danger")){var e=$(this).attr("title"),r=e.replace(/[ \/]/g,"");GV.addData(this,r)}else $(this).hasClass("plot_btn")&&GV.addData(this,"all")});

data/aux/files/js/src/plots.js

@@ -103,7 +103,7 @@ if (!GV) {
 
   GV.createChildRow = function ($currentRow, target, source) {
     var childRowHTML = '<tr class="tablesorter-childRow" id="mainrow' + target +
-                       '"><td colspan="12" id="row' + target + '"><div id="' +
+                       '"><td colspan="20" id="row' + target + '"><div id="' +
                        target + '" class="expanded-child"></div></td></tr>';
     $currentRow.addClass('tablesorter-hasChildRow');
     $currentRow.after(childRowHTML);

data/genevalidator.gemspec

@@ -26,7 +26,7 @@ Gem::Specification.new do |s|
   s.add_development_dependency('minitest', '~> 5.4')
   s.add_dependency('bio', '~> 1.4')
   s.add_dependency('bio-blastxmlparser', '~>2.0')
-  s.add_dependency('statsample', '1.4') # Updating to 1.5 breaks GV
+  s.add_dependency('statsample', '2.0.1')
 
   s.files         = `git ls-files -z`.split("\x0")
   s.executables   = s.files.grep(%r{^bin/}) { |f| File.basename(f) }

data/lib/genevalidator/arg_validation.rb

@@ -50,6 +50,8 @@ module GeneValidator
         @opt[:num_threads] = Integer(@opt[:num_threads])
         unless @opt[:num_threads] > 0
           $stderr.puts 'Number of threads can not be lower than 0'
+          $stderr.puts 'Setting number of threads to 1'
+          @opt[:num_threads] = 1
         end
         return unless @opt[:num_threads] > 256
         $stderr.puts "Number of threads set at #{@opt[:num_threads]} is" \

data/lib/genevalidator/ext/array.rb

@@ -34,4 +34,8 @@ end
 
 class Array
   include GeneValidator::ExtraArrayMethods
+
+  def mean
+    inject(:+).to_f / length
+  end
 end

data/lib/genevalidator/validation.rb

@@ -1,10 +1,14 @@
 require 'forwardable'
+# Statsample: must loaded before /ext/array as they modify a built-in class
+require 'statsample'
 
 require 'genevalidator/blast'
 require 'genevalidator/exceptions'
+require 'genevalidator/ext/array'
 require 'genevalidator/output'
 require 'genevalidator/pool'
 require 'genevalidator/query'
+require 'genevalidator/validation_maker_qi'
 require 'genevalidator/validation_length_cluster'
 require 'genevalidator/validation_length_rank'
 require 'genevalidator/validation_blast_reading_frame'
@@ -32,6 +36,8 @@ module GeneValidator
     def run_validations(iterator)
       p = Pool.new(@opt[:num_threads]) if @opt[:num_threads] > 1
 
+      check_if_maker_input?
+
       while @config[:idx] + 1 < @query_idx.length
         prediction = get_info_on_query_sequence
         @config[:idx] += 1
@@ -74,6 +80,20 @@ module GeneValidator
       prediction
     end
 
+    # Adds 'maker' to @opt[:validations] if the first definiton in the input
+    # fasta file contains MAKER's QI (quality index) score
+    def check_if_maker_input?(input_file = @opt[:input_fasta_file])
+      query        = IO.binread(input_file, @query_idx[1], @query_idx[0])
+      parse_query  = query.scan(/>([^\n]*)\n([A-Za-z\n]*)/)[0]
+      definition   = parse_query[0].gsub("\n", '')
+      number       = '\d*\.?\d*'
+      qi_match     = definition.match(/QI:#{number}\|#{number}\|#{number}\|
+                                      #{number}\|#{number}\|#{number}\|
+                                      #{number}\|#{number}\|#{number}/x)
+      return if qi_match.nil?
+      @opt[:validations] << 'maker_qi'
+    end
+
     def parse_next_iteration(iterator, prediction)
       iterator.next if @config[:idx] < @config[:start_idx]
       if @opt[:blast_xml_file]
@@ -159,18 +179,22 @@ module GeneValidator
 
     def create_validation_tests(prediction, hits)
       val = []
+      val.push MakerQIValidation.new(prediction, hits)
       val.push LengthClusterValidation.new(prediction, hits)
       val.push LengthRankValidation.new(prediction, hits)
       val.push GeneMergeValidation.new(prediction, hits)
       val.push DuplicationValidation.new(prediction, hits)
-      if @config[:type] == :nucleotide
-        val.push BlastReadingFrameValidation.new(prediction, hits)
-        val.push OpenReadingFrameValidation.new(prediction, hits)
-      end
+      init_nucleotide_only_validations(val, prediction, hits)
       val.push AlignmentValidation.new(prediction, hits)
       val.select { |v| @opt[:validations].include? v.cli_name.downcase }
     end
 
+    def init_nucleotide_only_validations(val, prediction, hits)
+      return unless @config[:type] == :nucleotide
+      val.push BlastReadingFrameValidation.new(prediction, hits)
+      val.push OpenReadingFrameValidation.new(prediction, hits)
+    end
+
     def check_validations(vals)
       # check the class type of the elements in the list
       vals.each { |v| fail ValidationClassError unless v.is_a? ValidationTest }

data/lib/genevalidator/validation_alignment.rb

@@ -444,7 +444,7 @@ module GeneValidator
                :align,
                'Missing/Extra sequences Validation: Multiple Align. &' \
                'Statistical model of hits',
-               'Conserved Region, Yellow',
+               'Aligned Hit Sequence, red; Conserved Region, Yellow',
                'Offset in the Alignment',
                '',
                ma.length + 1,

data/lib/genevalidator/validation_duplication.rb

@@ -251,9 +251,9 @@ module GeneValidator
     # wilcox test implementation from statsample ruby gem
     # many thanks to Claudio for helping us with the implementation!
     def wilcox_test(averages)
-      wilcox = Statsample::Test.wilcoxon_signed_rank(averages.to_scale,
-                                                     Array.new(averages.length,
-                                                               1).to_scale)
+      wilcox = Statsample::Test.wilcoxon_signed_rank(Daru::Vector.new(averages),
+                                                     Daru::Vector.new(Array.new(averages.length,
+                                                               1)))
 
       (averages.length < 15) ? wilcox.probability_exact : wilcox.probability_z
     end

data/lib/genevalidator/validation_maker_qi.rb

@@ -0,0 +1,108 @@
+require 'forwardable'
+
+require 'genevalidator/exceptions'
+require 'genevalidator/validation_report'
+require 'genevalidator/validation_test'
+
+module GeneValidator
+  ##
+  # Class that stores the validation output information
+  class MakerQIValidationOutput < ValidationReport
+    def initialize(short_header, header, description, splice_sites, exons,
+                   expected = :yes)
+      @short_header, @header, @description = short_header, header, description
+      @splice_sites = splice_sites
+      @exons        = exons
+      @expected     = expected
+      @result       = validation
+      @approach     = 'We obtain the fraction of splice sites and exons' \
+                      ' confirmed by EST/RNASeq alignment from the FASTA' \
+                      ' defline for MAKER predicted gene models. RNASeq is' \
+                      ' often best evidence to ascertain the quality of gene' \
+                      ' models'
+      @explanation  = explain
+      @conclusion   = conclude
+    end
+
+    def explain
+      "#{@exons}% of exons match an EST/mRNA-seq alignment and" \
+      " #{@splice_sites}% of splice sites are confirmed by EST/mRNA-seq" \
+      " alignment."
+    end
+
+    def conclude
+      if @result == :yes
+        'More than 80% of this gene is confirmed by RNASeq evidence.' \
+        'Thus, the MAKER Quality Index suggests that the query sequence is of' \
+        ' a good quality.'
+      else
+        'Less than 80% of this gene is confirmed by RNASeq evidence.' \
+        'Thus, the MAKER Quality Index suggests that there may be some issues'\
+        ' with the query seqeunce.'
+      end
+    end
+
+    def print
+      "Exons:&nbsp;#{@exons}%;" \
+      " Splice&nbsp;Sites:&nbsp;#{@splice_sites}%"
+    end
+
+    def validation
+      (@splice_sites > 80 && @exons > 80) ? :yes : :no
+    end
+  end
+
+  ##
+  # This class contains the methods necessary for
+  # reading frame validation based on BLAST output
+  class MakerQIValidation < ValidationTest
+    def initialize(type, prediction, hits = nil)
+      super
+      @short_header = 'QualityIndex'
+      @header       = 'Quality Index'
+      @description  = 'MAKER mRNA Quality Index'
+      @cli_name     = 'maker_qi'
+    end
+
+    ##
+    # Check reading frame inconsistency
+    # Params:
+    # +lst+: vector of +Sequence+ objects
+    # Output:
+    # +QIValidationOutput+ object
+    def run
+      fail unless prediction.is_a?(Query)
+
+      start  = Time.now
+
+      number = '\d*\.?\d*'
+      match  = @prediction.definition.match(/QI:#{number}\|(#{number})\|
+                                             (#{number})\|#{number}\|
+                                             #{number}\|#{number}\|#{number}\|
+                                             #{number}\|#{number}/x)
+
+      fail NotEnoughEvidence if match.nil?
+
+      # % of splice sites confirmed by EST/mRNA-seq alignment
+      splice_sites = (match[1].to_f * 100).round
+      # % of exons that match an EST/mRNA-seq alignment
+      exons = (match[2].to_f * 100).round
+
+      @validation_report = MakerQIValidationOutput.new(@short_header, @header,
+                                                       @description,
+                                                       splice_sites, exons)
+      @validation_report.run_time = Time.now - start
+      @validation_report
+
+    rescue NotEnoughEvidence
+      @validation_report =  ValidationReport.new('Not enough evidence',
+                                                 :warning, @short_header,
+                                                 @header, @description)
+    rescue
+      @validation_report = ValidationReport.new('Unexpected error', :error,
+                                                @short_header, @header,
+                                                @description)
+      @validation_report.errors.push 'Unexpected Error'
+    end
+  end
+end

data/lib/genevalidator/version.rb

@@ -1,3 +1,3 @@
 module GeneValidator
-  VERSION = '1.6.5'
+  VERSION = '1.6.6'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genevalidator
 version: !ruby/object:Gem::Version
-  version: 1.6.5
+  version: 1.6.6
 platform: ruby
 authors:
 - Monica Dragan
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-08-03 00:00:00.000000000 Z
+date: 2015-10-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -123,14 +123,14 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: 2.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: 2.0.1
 description: The tool validates the input predicted genes and provides useful information
   (length validation, gene merge validation, sequence duplication checking, ORF finding)
   based on the similarities to genes in public databases.
@@ -209,6 +209,7 @@ files:
 - lib/genevalidator/validation_gene_merge.rb
 - lib/genevalidator/validation_length_cluster.rb
 - lib/genevalidator/validation_length_rank.rb
+- lib/genevalidator/validation_maker_qi.rb
 - lib/genevalidator/validation_open_reading_frame.rb
 - lib/genevalidator/validation_report.rb
 - lib/genevalidator/validation_test.rb