genevalidator 1.6.1 → 1.6.2

data/test/test_validations.rb

@@ -11,13 +11,30 @@ require 'genevalidator/validation_gene_merge'
 require 'genevalidator/validation_duplication'
 require 'genevalidator/validation_open_reading_frame'
 require 'genevalidator/validation_alignment'
+require 'genevalidator/validation'
 
 module GeneValidator
+  class Validate
+    # Extend Validate Class with an alternative validate method that
+    #   doesn't produce the output and returns the output instance
+    def validate_without_output(prediction, hits, current_idx)
+      hits = remove_identical_hits(prediction, hits)
+      vals = create_validation_tests(prediction, hits)
+      check_validations(vals)
+      vals.each(&:run)
+      @run_output = Output.new(current_idx, hits.length, prediction.definition)
+      @run_output.validations = vals.map(&:validation_report)
+      check_validations_output(vals)
+      @run_output
+    end
+  end
+
+  # Test the output produced by the validations
   class ValidateOutput < Minitest::Test
     filename_fasta   = 'test/test_files/test_sequences.fasta'
     filename_xml     = "#{filename_fasta}.blast_xml"
     filename_xml_raw = "#{filename_fasta}.blast_xml.raw_seq"
-    FileUtils.rm_rf("#{filename_fasta}.html") rescue Error
+    FileUtils.rm_rf("#{filename_fasta}.html") rescue Errno::ENOENT
     opt = {
       input_fasta_file: filename_fasta,
       validations: ['all'],
@@ -26,11 +43,10 @@ module GeneValidator
       num_threads: 1,
       test: true
     }
-
-    val      = GeneValidator::Validation.new(opt)
+    GeneValidator.init(opt)
+    val      = GeneValidator::Validate.new
     xml      = File.open(filename_xml, 'rb').read
     iterator = Bio::BlastXMLParser::NokogiriBlastXml.new(xml).to_enum
-    val.create_an_index_file_of_raw_seq_file(opt[:raw_sequences])
 
     describe 'Detailed Validation of normal Insulin Query' do
       hits     = BlastUtils.parse_next(iterator, :nucleotide)
@@ -48,7 +64,7 @@ module GeneValidator
                                 'AAACTACTGCAACTAG'
 
       prediction.length_protein = 108
-      vals = val.do_validations(prediction, hits, 1).validations
+      vals = val.validate_without_output(prediction, hits, 1).validations
 
       lcv = vals.select { |v| v.class == LengthClusterValidationOutput }[0]
       lrv = vals.select { |v| v.class == LengthRankValidationOutput }[0]
@@ -96,7 +112,7 @@ module GeneValidator
       end
 
       it 'should validate blast reading frame' do
-        assert_equal({ 1 => 500 }, rfv.frames_histo)
+        assert_equal({ 1 => 500 }, rfv.frames)
         assert_equal(500, rfv.total_hsp)
         assert_equal(:yes, rfv.result)
       end
@@ -147,7 +163,7 @@ module GeneValidator
                                 'GAGCGGGG'
       prediction.length_protein = 46
 
-      vals = val.do_validations(prediction, hits, 1).validations
+      vals = val.validate_without_output(prediction, hits, 1).validations
 
       lcv = vals.select { |v| v.class == LengthClusterValidationOutput }[0]
       lrv = vals.select { |v| v.class == LengthRankValidationOutput }[0]
@@ -190,15 +206,15 @@ module GeneValidator
                                 'CAACTGGAAAACTACTGCAACTAG'
       prediction.length_protein = 46
 
-      validations = val.do_validations(prediction, hits, 1).validations
+      vals = val.validate_without_output(prediction, hits, 1).validations
 
-      lcv = validations.select { |v| v.class == LengthClusterValidationOutput }[0]
-      lrv = validations.select { |v| v.class == LengthRankValidationOutput }[0]
-      rfv = validations.select { |v| v.class == BlastRFValidationOutput }[0]
-      gmv = validations.select { |v| v.class == GeneMergeValidationOutput }[0]
-      dv  = validations.select { |v| v.class == DuplicationValidationOutput }[0]
-      av  = validations.select { |v| v.class == AlignmentValidationOutput }[0]
-      ov  = validations.select { |v| v.class == ORFValidationOutput }[0]
+      lcv = vals.select { |v| v.class == LengthClusterValidationOutput }[0]
+      lrv = vals.select { |v| v.class == LengthRankValidationOutput }[0]
+      rfv = vals.select { |v| v.class == BlastRFValidationOutput }[0]
+      gmv = vals.select { |v| v.class == GeneMergeValidationOutput }[0]
+      dv  = vals.select { |v| v.class == DuplicationValidationOutput }[0]
+      av  = vals.select { |v| v.class == AlignmentValidationOutput }[0]
+      ov  = vals.select { |v| v.class == ORFValidationOutput }[0]
 
       it 'should validate as expected' do
         assert_equal(:no, lcv.result)
@@ -232,15 +248,15 @@ module GeneValidator
                                 'AAGGCCGCTGCTTCGGGCCCAGCATCTGCTGCGCGGACGAGC'
       prediction.length_protein = 175
 
-      validations = val.do_validations(prediction, hits, 1).validations
+      vals = val.validate_without_output(prediction, hits, 1).validations
 
-      lcv = validations.select { |v| v.class == LengthClusterValidationOutput }[0]
-      lrv = validations.select { |v| v.class == LengthRankValidationOutput }[0]
-      rfv = validations.select { |v| v.class == BlastRFValidationOutput }[0]
-      gmv = validations.select { |v| v.class == GeneMergeValidationOutput }[0]
-      dv  = validations.select { |v| v.class == DuplicationValidationOutput }[0]
-      av  = validations.select { |v| v.class == AlignmentValidationOutput }[0]
-      ov  = validations.select { |v| v.class == ORFValidationOutput }[0]
+      lcv = vals.select { |v| v.class == LengthClusterValidationOutput }[0]
+      lrv = vals.select { |v| v.class == LengthRankValidationOutput }[0]
+      rfv = vals.select { |v| v.class == BlastRFValidationOutput }[0]
+      gmv = vals.select { |v| v.class == GeneMergeValidationOutput }[0]
+      dv  = vals.select { |v| v.class == DuplicationValidationOutput }[0]
+      av  = vals.select { |v| v.class == AlignmentValidationOutput }[0]
+      ov  = vals.select { |v| v.class == ORFValidationOutput }[0]
 
       it 'should validate length cluster validation' do
         assert_equal(:no, lcv.result)
@@ -320,15 +336,15 @@ module GeneValidator
                                 'AGATATTGTTAC'
       prediction.length_protein = 840
 
-      validations = val.do_validations(prediction, hits, 1).validations
+      vals = val.validate_without_output(prediction, hits, 1).validations
 
-      lcv = validations.select { |v| v.class == LengthClusterValidationOutput }[0]
-      lrv = validations.select { |v| v.class == LengthRankValidationOutput }[0]
-      rfv = validations.select { |v| v.class == BlastRFValidationOutput }[0]
-      gmv = validations.select { |v| v.class == GeneMergeValidationOutput }[0]
-      dv  = validations.select { |v| v.class == DuplicationValidationOutput }[0]
-      av  = validations.select { |v| v.class == AlignmentValidationOutput }[0]
-      ov  = validations.select { |v| v.class == ORFValidationOutput }[0]
+      lcv = vals.select { |v| v.class == LengthClusterValidationOutput }[0]
+      lrv = vals.select { |v| v.class == LengthRankValidationOutput }[0]
+      rfv = vals.select { |v| v.class == BlastRFValidationOutput }[0]
+      gmv = vals.select { |v| v.class == GeneMergeValidationOutput }[0]
+      dv  = vals.select { |v| v.class == DuplicationValidationOutput }[0]
+      av  = vals.select { |v| v.class == AlignmentValidationOutput }[0]
+      ov  = vals.select { |v| v.class == ORFValidationOutput }[0]
 
       it 'should validate length cluster validation' do
         assert_equal(:no, lcv.result)
@@ -340,6 +356,6 @@ module GeneValidator
         assert_equal(:no, av.result)
       end
     end
-    FileUtils.rm_rf("#{filename_fasta}.html") rescue Error
+    FileUtils.rm_rf("#{filename_fasta}.html") rescue Errno::ENOENT
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genevalidator
 version: !ruby/object:Gem::Version
-  version: 1.6.1
+  version: 1.6.2
 platform: ruby
 authors:
 - Monica Dragan
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-31 00:00:00.000000000 Z
+date: 2015-07-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -41,6 +41,40 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: codeclimate-test-reporter
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.4'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.4.7
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.4'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.4.7
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
@@ -87,18 +121,19 @@ dependencies:
   name: statsample
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
         version: '1.4'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
         version: '1.4'
-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.
+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.
 email: y.wurm@qmul.ac.uk
 executables:
 - genevalidator
@@ -129,6 +164,9 @@ files:
 - aux/files/js/plots.js
 - aux/files/js/script.js
 - aux/files/json/.gitkeep
+- aux/json_footer.erb
+- aux/json_header.erb
+- aux/json_query.erb
 - aux/template_footer.erb
 - aux/template_header.erb
 - aux/template_query.erb
@@ -140,65 +178,6 @@ files:
 - data/protein_data.fasta
 - data/protein_data.fasta.blast_tabular
 - data/protein_data.fasta.blast_xml
-- doc/AliasDuplicationError.html
-- doc/AlignmentValidation.html
-- doc/AlignmentValidationOutput.html
-- doc/Blast.html
-- doc/BlastRFValidationOutput.html
-- doc/BlastReadingFrameValidation.html
-- doc/BlastUtils.html
-- doc/ClasspathError.html
-- doc/Cluster.html
-- doc/DuplciationValidationOutput.html
-- doc/DuplicationValidation.html
-- doc/DuplicationValidationOutput.html
-- doc/FileNotFoundException.html
-- doc/GeneMergeValidation.html
-- doc/GeneMergeValidationOutput.html
-- doc/HierarchicalClusterization.html
-- doc/Hsp.html
-- doc/InconsistentTabularFormat.html
-- doc/LengthClusterValidation.html
-- doc/LengthClusterValidationOutput.html
-- doc/LengthRankValidation.html
-- doc/LengthRankValidationOutput.html
-- doc/NoInternetError.html
-- doc/NoMafftInstallationError.html
-- doc/NoPIdentError.html
-- doc/NoValidationError.html
-- doc/NotEnoughHitsError.html
-- doc/ORFValidationOutput.html
-- doc/OpenReadingFrameValidation.html
-- doc/OtherError.html
-- doc/Output.html
-- doc/Pair.html
-- doc/PairCluster.html
-- doc/Plot.html
-- doc/QueryError.html
-- doc/ReportClassError.html
-- doc/Sequence.html
-- doc/SequenceTypeError.html
-- doc/TabularEntry.html
-- doc/TabularParser.html
-- doc/Validation.html
-- doc/ValidationClassError.html
-- doc/ValidationOutput.html
-- doc/ValidationReport.html
-- doc/ValidationTest.html
-- doc/_index.html
-- doc/class_list.html
-- doc/css/common.css
-- doc/css/full_list.css
-- doc/css/style.css
-- doc/file.README.html
-- doc/file_list.html
-- doc/frames.html
-- doc/index.html
-- doc/js/app.js
-- doc/js/full_list.js
-- doc/js/jquery.js
-- doc/method_list.html
-- doc/top-level-namespace.html
 - genevalidator.gemspec
 - lib/genevalidator.rb
 - lib/genevalidator/arg_validation.rb
@@ -208,10 +187,12 @@ files:
 - lib/genevalidator/ext/array.rb
 - lib/genevalidator/get_raw_sequences.rb
 - lib/genevalidator/hsp.rb
+- lib/genevalidator/json_to_gv_results.rb
 - lib/genevalidator/output.rb
 - lib/genevalidator/pool.rb
 - lib/genevalidator/sequences.rb
 - lib/genevalidator/tabular_parser.rb
+- lib/genevalidator/validation.rb
 - lib/genevalidator/validation_alignment.rb
 - lib/genevalidator/validation_blast_reading_frame.rb
 - lib/genevalidator/validation_duplication.rb
@@ -228,24 +209,20 @@ files:
 - test/test_clusterization.rb
 - test/test_clusterization_2d.rb
 - test/test_extended_array_methods.rb
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.index
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq.idx
-- test/test_files/all_validations_prot/all_validations_prot.fasta
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq.idx
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.index
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.raw_seq
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.raw_seq.idx
+- test/test_files/all_validations_mrna/mrna.blast_tab6
+- test/test_files/all_validations_mrna/mrna.blast_tab7
+- test/test_files/all_validations_mrna/mrna.blast_xml
+- test/test_files/all_validations_mrna/mrna.blast_xml.index
+- test/test_files/all_validations_mrna/mrna.fa
+- test/test_files/all_validations_mrna/mrna.raw_seq
+- test/test_files/all_validations_mrna/mrna.raw_seq.idx
+- test/test_files/all_validations_prot/prot.blast_tab6
+- test/test_files/all_validations_prot/prot.blast_tab7
+- test/test_files/all_validations_prot/prot.blast_xml
+- test/test_files/all_validations_prot/prot.blast_xml.index
+- test/test_files/all_validations_prot/prot.fa
+- test/test_files/all_validations_prot/prot.raw_seq
+- test/test_files/all_validations_prot/prot.raw_seq.idx
 - test/test_files/mixed_type.fasta
 - test/test_files/ncbi_mrna.tab.20
 - test/test_files/ncbi_mrna.xml.20
@@ -294,7 +271,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.6
+rubygems_version: 2.4.8
 signing_key: 
 specification_version: 4
 summary: Identifying problems with gene predictions.
@@ -305,24 +282,20 @@ test_files:
 - test/test_clusterization.rb
 - test/test_clusterization_2d.rb
 - test/test_extended_array_methods.rb
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.index
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq
-- test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq.idx
-- test/test_files/all_validations_prot/all_validations_prot.fasta
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq.idx
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.index
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.raw_seq
-- test/test_files/all_validations_prot/all_validations_prot.fasta.blast_xml.raw_seq.idx
+- test/test_files/all_validations_mrna/mrna.blast_tab6
+- test/test_files/all_validations_mrna/mrna.blast_tab7
+- test/test_files/all_validations_mrna/mrna.blast_xml
+- test/test_files/all_validations_mrna/mrna.blast_xml.index
+- test/test_files/all_validations_mrna/mrna.fa
+- test/test_files/all_validations_mrna/mrna.raw_seq
+- test/test_files/all_validations_mrna/mrna.raw_seq.idx
+- test/test_files/all_validations_prot/prot.blast_tab6
+- test/test_files/all_validations_prot/prot.blast_tab7
+- test/test_files/all_validations_prot/prot.blast_xml
+- test/test_files/all_validations_prot/prot.blast_xml.index
+- test/test_files/all_validations_prot/prot.fa
+- test/test_files/all_validations_prot/prot.raw_seq
+- test/test_files/all_validations_prot/prot.raw_seq.idx
 - test/test_files/mixed_type.fasta
 - test/test_files/ncbi_mrna.tab.20
 - test/test_files/ncbi_mrna.xml.20
@@ -340,3 +313,4 @@ test_files:
 - test/test_sequences.rb
 - test/test_validation_open_reading_frame.rb
 - test/test_validations.rb
+has_rdoc: 

data/doc/AliasDuplicationError.html

@@ -1,134 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Exception: AliasDuplicationError
-  
-    &mdash; Documentation by YARD 0.8.7.2
-  
-</title>
-
-  <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
-
-  <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
-
-<script type="text/javascript" charset="utf-8">
-  hasFrames = window.top.frames.main ? true : false;
-  relpath = '';
-  framesUrl = "frames.html#!" + escape(window.location.href);
-</script>
-
-
-  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
-
-  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
-
-
-  </head>
-  <body>
-    <div id="header">
-      <div id="menu">
-  
-    <a href="_index.html">Index (A)</a> &raquo;
-    
-    
-    <span class="title">AliasDuplicationError</span>
-  
-
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-
-      <div id="search">
-  
-    <a class="full_list_link" id="class_list_link"
-        href="class_list.html">
-      Class List
-    </a>
-  
-    <a class="full_list_link" id="method_list_link"
-        href="method_list.html">
-      Method List
-    </a>
-  
-    <a class="full_list_link" id="file_list_link"
-        href="file_list.html">
-      File List
-    </a>
-  
-</div>
-      <div class="clear"></div>
-    </div>
-
-    <iframe id="search_frame"></iframe>
-
-    <div id="content"><h1>Exception: AliasDuplicationError
-  
-  
-  
-</h1>
-
-<dl class="box">
-  
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName">Exception</span>
-      
-        <ul class="fullTree">
-          <li>Object</li>
-          
-            <li class="next">Exception</li>
-          
-            <li class="next">AliasDuplicationError</li>
-          
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      
-      </dd>
-    
-  
-  
-    
-  
-    
-  
-  
-  
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/exceptions.rb</dd>
-  
-</dl>
-<div class="clear"></div>
-
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-    
-<p>Exception raised when the are alias duplications</p>
-
-
-  </div>
-</div>
-<div class="tags">
-  
-
-</div>
-
-
-
-
-
-
-
-  
-
-</div>
-
-    <div id="footer">
-  Generated on Sat Sep 28 07:01:32 2013 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.2 (ruby-1.9.3).
-</div>
-
-  </body>
-</html>