RubyGems - genevalidator - Versions diffs - 1.6.1 → 1.6.2 - Mend

genevalidator 1.6.1 → 1.6.2

Files changed (131) hide show

checksums.yaml +4 -4
data/.gitignore +3 -1
data/.travis.yml +2 -0
data/README.md +78 -30
data/Rakefile +11 -8
data/aux/app_template_footer.erb +1 -6
data/aux/app_template_header.erb +12 -32
data/aux/files/css/style.css +2 -8
data/aux/files/js/plots.js +564 -576
data/aux/files/js/script.js +10 -0
data/aux/json_footer.erb +8 -0
data/aux/json_header.erb +19 -0
data/aux/json_query.erb +14 -0
data/aux/template_footer.erb +9 -58
data/aux/template_header.erb +18 -58
data/aux/template_query.erb +8 -36
data/bin/genevalidator +45 -32
data/genevalidator.gemspec +11 -7
data/lib/genevalidator.rb +75 -455
data/lib/genevalidator/arg_validation.rb +78 -107
data/lib/genevalidator/blast.rb +57 -60
data/lib/genevalidator/clusterization.rb +15 -15
data/lib/genevalidator/exceptions.rb +32 -5
data/lib/genevalidator/get_raw_sequences.rb +70 -33
data/lib/genevalidator/hsp.rb +1 -4
data/lib/genevalidator/json_to_gv_results.rb +109 -0
data/lib/genevalidator/output.rb +177 -185
data/lib/genevalidator/pool.rb +2 -1
data/lib/genevalidator/sequences.rb +3 -3
data/lib/genevalidator/tabular_parser.rb +24 -18
data/lib/genevalidator/validation.rb +279 -0
data/lib/genevalidator/validation_alignment.rb +31 -47
data/lib/genevalidator/validation_blast_reading_frame.rb +19 -18
data/lib/genevalidator/validation_duplication.rb +23 -19
data/lib/genevalidator/validation_gene_merge.rb +30 -65
data/lib/genevalidator/validation_length_cluster.rb +14 -53
data/lib/genevalidator/validation_length_rank.rb +10 -11
data/lib/genevalidator/validation_open_reading_frame.rb +18 -19
data/lib/genevalidator/validation_report.rb +2 -5
data/lib/genevalidator/validation_test.rb +8 -4
data/lib/genevalidator/version.rb +1 -1
data/test/test_all_validations.rb +51 -66
data/test/test_blast.rb +68 -51
data/test/test_clusterization.rb +1 -1
data/test/test_clusterization_2d.rb +19 -13
data/test/test_extended_array_methods.rb +1 -1
data/test/test_files/all_validations_mrna/mrna.blast_tab6 +1806 -0
data/test/test_files/all_validations_mrna/mrna.blast_tab7 +1865 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml → mrna.blast_xml} +18642 -1
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.index → mrna.blast_xml.index} +300 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta → mrna.fa} +0 -0
data/test/test_files/all_validations_mrna/mrna.raw_seq +3970 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.raw_seq.idx → mrna.raw_seq.idx} +901 -1
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_tab → prot.blast_tab6} +416 -0
data/test/test_files/all_validations_prot/prot.blast_tab7 +2400 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml → prot.blast_xml} +18299 -6723
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.index → prot.blast_xml.index} +408 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta → prot.fa} +0 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq → prot.raw_seq} +2735 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq.idx → prot.raw_seq.idx} +3032 -1808
data/test/test_sequences.rb +46 -41
data/test/test_validation_open_reading_frame.rb +318 -202
data/test/test_validations.rb +48 -32
metadata +76 -102
data/doc/AliasDuplicationError.html +0 -134
data/doc/AlignmentValidation.html +0 -1687
data/doc/AlignmentValidationOutput.html +0 -659
data/doc/Blast.html +0 -1905
data/doc/BlastRFValidationOutput.html +0 -545
data/doc/BlastReadingFrameValidation.html +0 -370
data/doc/BlastUtils.html +0 -875
data/doc/ClasspathError.html +0 -134
data/doc/Cluster.html +0 -1316
data/doc/DuplciationValidationOutput.html +0 -564
data/doc/DuplicationValidation.html +0 -920
data/doc/DuplicationValidationOutput.html +0 -564
data/doc/FileNotFoundException.html +0 -134
data/doc/GeneMergeValidation.html +0 -935
data/doc/GeneMergeValidationOutput.html +0 -652
data/doc/HierarchicalClusterization.html +0 -994
data/doc/Hsp.html +0 -1485
data/doc/InconsistentTabularFormat.html +0 -135
data/doc/LengthClusterValidation.html +0 -982
data/doc/LengthClusterValidationOutput.html +0 -515
data/doc/LengthRankValidation.html +0 -496
data/doc/LengthRankValidationOutput.html +0 -517
data/doc/NoInternetError.html +0 -135
data/doc/NoMafftInstallationError.html +0 -134
data/doc/NoPIdentError.html +0 -134
data/doc/NoValidationError.html +0 -134
data/doc/NotEnoughHitsError.html +0 -135
data/doc/ORFValidationOutput.html +0 -593
data/doc/OpenReadingFrameValidation.html +0 -1107
data/doc/OtherError.html +0 -123
data/doc/Output.html +0 -1540
data/doc/Pair.html +0 -309
data/doc/PairCluster.html +0 -767
data/doc/Plot.html +0 -837
data/doc/QueryError.html +0 -134
data/doc/ReportClassError.html +0 -135
data/doc/Sequence.html +0 -1299
data/doc/SequenceTypeError.html +0 -135
data/doc/TabularEntry.html +0 -837
data/doc/TabularParser.html +0 -1104
data/doc/Validation.html +0 -2147
data/doc/ValidationClassError.html +0 -134
data/doc/ValidationOutput.html +0 -460
data/doc/ValidationReport.html +0 -940
data/doc/ValidationTest.html +0 -939
data/doc/_index.html +0 -449
data/doc/class_list.html +0 -54
data/doc/css/common.css +0 -1
data/doc/css/full_list.css +0 -57
data/doc/css/style.css +0 -338
data/doc/file.README.html +0 -151
data/doc/file_list.html +0 -56
data/doc/frames.html +0 -26
data/doc/index.html +0 -151
data/doc/js/app.js +0 -214
data/doc/js/full_list.js +0 -178
data/doc/js/jquery.js +0 -4
data/doc/method_list.html +0 -1505
data/doc/top-level-namespace.html +0 -112
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab +0 -967
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index +0 -967
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq +0 -4929
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx +0 -1006
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq +0 -2075
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index +0 -1864
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq +0 -42411
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq.idx +0 -3751

@@ -1,2147 +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>
-  Class: Validation
-    &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 (V)</a> &raquo;
-    <span class="title">Validation</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>Class: Validation
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName">Object</span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next">Validation</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/validation.rb</dd>
-</dl>
-<div class="clear"></div>
-  <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
-  <ul class="summary">
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#all_query_outputs-instance_method" title="#all_query_outputs (instance method)">- (Object) <strong>all_query_outputs</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>list with all validation reports.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#fasta_filepath-instance_method" title="#fasta_filepath (instance method)">- (Object) <strong>fasta_filepath</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute fasta_filepath.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#filename-instance_method" title="#filename (instance method)">- (Object) <strong>filename</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute filename.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#html_path-instance_method" title="#html_path (instance method)">- (Object) <strong>html_path</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute html_path.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#idx-instance_method" title="#idx (instance method)">- (Object) <strong>idx</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>current number of the querry processed.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#mafft_path-instance_method" title="#mafft_path (instance method)">- (Object) <strong>mafft_path</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute mafft_path.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#query_offset_lst-instance_method" title="#query_offset_lst (instance method)">- (Object) <strong>query_offset_lst</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>array of indexes for the start offsets of each query in the fasta file.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#raw_seq_file_index-instance_method" title="#raw_seq_file_index (instance method)">- (Object) <strong>raw_seq_file_index</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute raw_seq_file_index.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#start_idx-instance_method" title="#start_idx (instance method)">- (Object) <strong>start_idx</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute start_idx.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#tabular_format-instance_method" title="#tabular_format (instance method)">- (Object) <strong>tabular_format</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute tabular_format.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#type-instance_method" title="#type (instance method)">- (Object) <strong>type</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute type.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#vlist-instance_method" title="#vlist (instance method)">- (Object) <strong>vlist</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute vlist.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#yaml_path-instance_method" title="#yaml_path (instance method)">- (Object) <strong>yaml_path</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute yaml_path.</p>
-</div></span>
-</li>
-  </ul>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#do_validations-instance_method" title="#do_validations (instance method)">- (Object) <strong>do_validations</strong>(prediction, hits) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Runs all the validations and prints the outputs given the current
-prediction query and the corresponding hits Params: <tt>hits</tt>: Array of
-<tt>Sequence</tt> objects Output: Array <tt>Output</tt> object.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#initialize-instance_method" title="#initialize (instance method)">- (Validation) <strong>initialize</strong>(fasta_filepath, vlist = [&quot;all&quot;], tabular_format = nil, xml_file = nil, raw_seq_file = nil, mafft_path = nil, start_idx = 1) </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Initilizes the object Params: <tt>fasta_filepath</tt>: fasta file with
-query sequences <tt>vlist</tt>: list of validations
-<tt>tabular_format</tt>: list of column names for parsing the tablar blast
-output <tt>xml_file</tt>: name of the precalculated blast xml output (used
-in 'skip blast' case) <tt>mafft_path</tt>: path of the MAFFT program
-installation <tt>start_idx</tt>: number of the sequence from the file to
-start with.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#parse_output-instance_method" title="#parse_output (instance method)">- (Object) <strong>parse_output</strong>(output) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Parses the blast output: autodetect the format: xml or tabular  Param:
-<tt>output</tt>: <tt>String</tt> with the blast output.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#remove_identical_hits-instance_method" title="#remove_identical_hits (instance method)">- (Object) <strong>remove_identical_hits</strong>(prediction, hits) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Removes identical hits Params: <tt>prediction</tt>: Sequence object
-<tt>hits</tt>: Array of <tt>Sequence</tt> objects Output: new array of hit
-<tt>Sequence</tt> objects.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#validation-instance_method" title="#validation (instance method)">- (Object) <strong>validation</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Parse the blast output and run validations.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#which-instance_method" title="#which (instance method)">- (Object) <strong>which</strong>(cmd) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>The ruby equivalent for 'which' command in unix.</p>
-</div></span>
-</li>
-    </ul>
-<div id="constructor_details" class="method_details_list">
-  <h2>Constructor Details</h2>
-    <div class="method_details first">
-  <h3 class="signature first" id="initialize-instance_method">
-    - (<tt><span class='object_link'><a href="" title="Validation (class)">Validation</a></span></tt>) <strong>initialize</strong>(fasta_filepath, vlist = [&quot;all&quot;], tabular_format = nil, xml_file = nil, raw_seq_file = nil, mafft_path = nil, start_idx = 1)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Initilizes the object Params: <tt>fasta_filepath</tt>: fasta file with
-query sequences <tt>vlist</tt>: list of validations
-<tt>tabular_format</tt>: list of column names for parsing the tablar blast
-output <tt>xml_file</tt>: name of the precalculated blast xml output (used
-in 'skip blast' case) <tt>mafft_path</tt>: path of the MAFFT program
-installation <tt>start_idx</tt>: number of the sequence from the file to
-start with</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 50</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span> <span class='id identifier rubyid_fasta_filepath'>fasta_filepath</span><span class='comma'>,</span>
-                <span class='id identifier rubyid_vlist'>vlist</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>all</span><span class='tstring_end'>&quot;</span></span><span class='rbracket'>]</span><span class='comma'>,</span>
-                <span class='id identifier rubyid_tabular_format'>tabular_format</span> <span class='op'>=</span> <span class='kw'>nil</span><span class='comma'>,</span>
-                <span class='id identifier rubyid_xml_file'>xml_file</span> <span class='op'>=</span> <span class='kw'>nil</span><span class='comma'>,</span>
-                <span class='id identifier rubyid_raw_seq_file'>raw_seq_file</span> <span class='op'>=</span> <span class='kw'>nil</span><span class='comma'>,</span>
-                <span class='id identifier rubyid_mafft_path'>mafft_path</span> <span class='op'>=</span> <span class='kw'>nil</span><span class='comma'>,</span>
-                <span class='id identifier rubyid_start_idx'>start_idx</span> <span class='op'>=</span> <span class='int'>1</span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-    <span class='ivar'>@fasta_filepath</span> <span class='op'>=</span> <span class='id identifier rubyid_fasta_filepath'>fasta_filepath</span>
-    <span class='ivar'>@xml_file</span> <span class='op'>=</span> <span class='id identifier rubyid_xml_file'>xml_file</span>
-    <span class='ivar'>@vlist</span> <span class='op'>=</span> <span class='id identifier rubyid_vlist'>vlist</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>^\s</span><span class='regexp_end'>/</span></span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\s\Z</span><span class='regexp_end'>/</span></span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\s</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-    <span class='ivar'>@idx</span> <span class='op'>=</span> <span class='int'>0</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_start_idx'>start_idx</span> <span class='op'>==</span> <span class='kw'>nil</span>
-      <span class='ivar'>@start_idx</span> <span class='op'>=</span> <span class='int'>1</span>
-    <span class='kw'>else</span>
-      <span class='ivar'>@start_idx</span> <span class='op'>=</span> <span class='id identifier rubyid_start_idx'>start_idx</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>FileNotFoundException</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='kw'>unless</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_exists?'>exists?</span><span class='lparen'>(</span><span class='ivar'>@fasta_filepath</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_fasta_content'>fasta_content</span> <span class='op'>=</span> <span class='const'>IO</span><span class='period'>.</span><span class='id identifier rubyid_binread'>binread</span><span class='lparen'>(</span><span class='ivar'>@fasta_filepath</span><span class='rparen'>)</span><span class='semicolon'>;</span>
-    <span class='comment'># the expected type for the sequences is the
-</span>    <span class='comment'># type of the first query
-</span>
-    <span class='comment'># autodetect the type of the sequence in the FASTA
-</span>    <span class='comment'># also check if the fasta file contains a single type of queries
-</span>    <span class='ivar'>@type</span> <span class='op'>=</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_type_of_sequences'>type_of_sequences</span><span class='lparen'>(</span><span class='id identifier rubyid_fasta_content'>fasta_content</span><span class='rparen'>)</span>
-    <span class='comment'># create a list of index of the queries in the FASTA
-</span>    <span class='ivar'>@query_offset_lst</span> <span class='op'>=</span> <span class='id identifier rubyid_fasta_content'>fasta_content</span><span class='period'>.</span><span class='id identifier rubyid_enum_for'>enum_for</span><span class='lparen'>(</span><span class='symbol'>:scan</span><span class='comma'>,</span> <span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>(&gt;[^&gt;]+)</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span> <span class='const'>Regexp</span><span class='period'>.</span><span class='id identifier rubyid_last_match'>last_match</span><span class='period'>.</span><span class='id identifier rubyid_begin'>begin</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span><span class='rbrace'>}</span>
-    <span class='ivar'>@query_offset_lst</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_fasta_content'>fasta_content</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_fasta_content'>fasta_content</span>   <span class='op'>=</span> <span class='kw'>nil</span> <span class='comment'># free memory for variable fasta_content
-</span>    <span class='ivar'>@tabular_format</span> <span class='op'>=</span> <span class='id identifier rubyid_tabular_format'>tabular_format</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_mafft_path'>mafft_path</span> <span class='op'>==</span> <span class='kw'>nil</span>
-      <span class='ivar'>@mafft_path</span> <span class='op'>=</span> <span class='id identifier rubyid_which'>which</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>mafft</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-    <span class='kw'>else</span>
-      <span class='ivar'>@mafft_path</span> <span class='op'>=</span> <span class='id identifier rubyid_mafft_path'>mafft_path</span>
-    <span class='kw'>end</span>
-    <span class='kw'>begin</span>
-      <span class='comment'># index raw_sequence file
-</span>      <span class='kw'>if</span> <span class='id identifier rubyid_raw_seq_file'>raw_seq_file</span> <span class='op'>!=</span> <span class='kw'>nil</span>
-        <span class='id identifier rubyid_raise'>raise</span> <span class='const'>FileNotFoundException</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span> <span class='kw'>unless</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_exists?'>exists?</span><span class='lparen'>(</span><span class='id identifier rubyid_raw_seq_file'>raw_seq_file</span><span class='rparen'>)</span>
-        <span class='comment'># leave only the identifiers in the fasta description
-</span>        <span class='id identifier rubyid_content'>content</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_raw_seq_file'>raw_seq_file</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>rb</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_read'>read</span>
-        <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_raw_seq_file'>raw_seq_file</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>w+</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_file'>file</span><span class='op'>|</span> <span class='id identifier rubyid_file'>file</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='id identifier rubyid_content'>content</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'> .*</span><span class='regexp_end'>/</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='rparen'>)</span><span class='rbrace'>}</span>
-        <span class='comment'>#index the fasta file
-</span>        <span class='id identifier rubyid_keys'>keys</span> <span class='op'>=</span> <span class='id identifier rubyid_content'>content</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>&gt;(.*)\n</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-        <span class='id identifier rubyid_values'>values</span> <span class='op'>=</span> <span class='id identifier rubyid_content'>content</span><span class='period'>.</span><span class='id identifier rubyid_enum_for'>enum_for</span><span class='lparen'>(</span><span class='symbol'>:scan</span><span class='comma'>,</span> <span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>(&gt;[^&gt;]+)</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span> <span class='const'>Regexp</span><span class='period'>.</span><span class='id identifier rubyid_last_match'>last_match</span><span class='period'>.</span><span class='id identifier rubyid_begin'>begin</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span><span class='rbrace'>}</span>
-        <span class='comment'># make am index hash
-</span>        <span class='id identifier rubyid_index_hash'>index_hash</span> <span class='op'>=</span> <span class='lbrace'>{</span><span class='rbrace'>}</span>
-        <span class='id identifier rubyid_index_hash'>index_hash</span> <span class='op'>=</span> <span class='id identifier rubyid_keys'>keys</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_index_hash'>index_hash</span><span class='lbracket'>[</span><span class='id identifier rubyid_keys'>keys</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_values'>values</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='rbrace'>}</span>
-        <span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_index_hash'>index_hash</span>
-        <span class='comment'># create FASTA index
-</span>        <span class='ivar'>@raw_seq_file_index</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_raw_seq_file'>raw_seq_file</span><span class='rbrace'>}</span><span class='tstring_content'>.idx</span><span class='tstring_end'>&quot;</span></span>
-      <span class='kw'>end</span>
-      <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-        <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-          <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: your file with raw sequences is not FASTA. Please use get_raw_sequences executable to create a correct one.\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>end</span>
-    <span class='comment'># build the path of html folder output
-</span>    <span class='id identifier rubyid_path'>path</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_dirname'>dirname</span><span class='lparen'>(</span><span class='ivar'>@fasta_filepath</span><span class='rparen'>)</span>
-    <span class='ivar'>@html_path</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_fasta_filepath'>fasta_filepath</span><span class='rbrace'>}</span><span class='tstring_content'>.html</span><span class='tstring_end'>&quot;</span></span>
-    <span class='ivar'>@yaml_path</span> <span class='op'>=</span> <span class='id identifier rubyid_path'>path</span>
-    <span class='ivar'>@filename</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_basename'>basename</span><span class='lparen'>(</span><span class='ivar'>@fasta_filepath</span><span class='rparen'>)</span><span class='comment'>#.scan(/\/([^\/]+)$/)[0][0]
-</span>    <span class='ivar'>@all_query_outputs</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-    <span class='comment'># create 'html' directory
-</span>    <span class='const'>FileUtils</span><span class='period'>.</span><span class='id identifier rubyid_rm_rf'>rm_rf</span><span class='lparen'>(</span><span class='ivar'>@html_path</span><span class='rparen'>)</span>
-    <span class='const'>Dir</span><span class='period'>.</span><span class='id identifier rubyid_mkdir'>mkdir</span><span class='lparen'>(</span><span class='ivar'>@html_path</span><span class='rparen'>)</span>
-    <span class='comment'># copy auxiliar folders to the html folder
-</span>    <span class='const'>FileUtils</span><span class='period'>.</span><span class='id identifier rubyid_cp_r'>cp_r</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/css</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='ivar'>@html_path</span><span class='rparen'>)</span>
-    <span class='const'>FileUtils</span><span class='period'>.</span><span class='id identifier rubyid_cp_r'>cp_r</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/js</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='ivar'>@html_path</span><span class='rparen'>)</span>
-    <span class='const'>FileUtils</span><span class='period'>.</span><span class='id identifier rubyid_cp_r'>cp_r</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/img</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='ivar'>@html_path</span><span class='rparen'>)</span>
-    <span class='const'>FileUtils</span><span class='period'>.</span><span class='id identifier rubyid_cp_r'>cp_r</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/font</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='ivar'>@html_path</span><span class='rparen'>)</span>
-    <span class='const'>FileUtils</span><span class='period'>.</span><span class='id identifier rubyid_cp_r'>cp_r</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/doc</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='ivar'>@html_path</span><span class='rparen'>)</span>
-  <span class='kw'>rescue</span> <span class='const'>SequenceTypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Sequence Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-     <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: input file containes mixed sequence types.\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit'>exit</span>
-  <span class='kw'>rescue</span> <span class='const'>FileNotFoundException</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>File not found error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>.</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-     <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: input file does not exist.\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit'>exit</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-</div>
-  <div id="instance_attr_details" class="attr_details">
-    <h2>Instance Attribute Details</h2>
-      <span id=""></span>
-      <div class="method_details first">
-  <h3 class="signature first" id="all_query_outputs-instance_method">
-    - (<tt>Object</tt>) <strong>all_query_outputs</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>list with all validation reports</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-36
-37
-38</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 36</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span>
-  <span class='ivar'>@all_query_outputs</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="fasta_filepath-instance_method">
-    - (<tt>Object</tt>) <strong>fasta_filepath</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute fasta_filepath</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-24
-25
-26</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 24</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_fasta_filepath'>fasta_filepath</span>
-  <span class='ivar'>@fasta_filepath</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="filename-instance_method">
-    - (<tt>Object</tt>) <strong>filename</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute filename</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-28
-29
-30</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 28</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_filename'>filename</span>
-  <span class='ivar'>@filename</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="html_path-instance_method">
-    - (<tt>Object</tt>) <strong>html_path</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute html_path</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-25
-26
-27</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 25</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_html_path'>html_path</span>
-  <span class='ivar'>@html_path</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="idx=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="idx-instance_method">
-    - (<tt>Object</tt>) <strong>idx</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>current number of the querry processed</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-31
-32
-33</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 31</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_idx'>idx</span>
-  <span class='ivar'>@idx</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="mafft_path-instance_method">
-    - (<tt>Object</tt>) <strong>mafft_path</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute mafft_path</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-27
-28
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 27</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_mafft_path'>mafft_path</span>
-  <span class='ivar'>@mafft_path</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="query_offset_lst-instance_method">
-    - (<tt>Object</tt>) <strong>query_offset_lst</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>array of indexes for the start offsets of each query in the fasta file</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-34
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 34</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_query_offset_lst'>query_offset_lst</span>
-  <span class='ivar'>@query_offset_lst</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="raw_seq_file_index-instance_method">
-    - (<tt>Object</tt>) <strong>raw_seq_file_index</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute raw_seq_file_index</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-29
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 29</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_raw_seq_file_index'>raw_seq_file_index</span>
-  <span class='ivar'>@raw_seq_file_index</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="start_idx-instance_method">
-    - (<tt>Object</tt>) <strong>start_idx</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute start_idx</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-32
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 32</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_start_idx'>start_idx</span>
-  <span class='ivar'>@start_idx</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="tabular_format-instance_method">
-    - (<tt>Object</tt>) <strong>tabular_format</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute tabular_format</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-39
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 39</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_tabular_format'>tabular_format</span>
-  <span class='ivar'>@tabular_format</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="type-instance_method">
-    - (<tt>Object</tt>) <strong>type</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute type</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-23
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 23</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_type'>type</span>
-  <span class='ivar'>@type</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="vlist-instance_method">
-    - (<tt>Object</tt>) <strong>vlist</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute vlist</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 38</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_vlist'>vlist</span>
-  <span class='ivar'>@vlist</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="yaml_path-instance_method">
-    - (<tt>Object</tt>) <strong>yaml_path</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute yaml_path</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-26
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 26</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_yaml_path'>yaml_path</span>
-  <span class='ivar'>@yaml_path</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="do_validations-instance_method">
-    - (<tt>Object</tt>) <strong>do_validations</strong>(prediction, hits)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Runs all the validations and prints the outputs given the current
-prediction query and the corresponding hits Params: <tt>hits</tt>: Array of
-<tt>Sequence</tt> objects Output: Array <tt>Output</tt> object</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 320</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_do_validations'>do_validations</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-  <span class='kw'>begin</span>
-    <span class='id identifier rubyid_hits'>hits</span> <span class='op'>=</span> <span class='id identifier rubyid_remove_identical_hits'>remove_identical_hits</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='rparen'>)</span>
-    <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span> <span class='comment'>#NoPIdentError
-</span>  <span class='kw'>end</span>
-  <span class='comment'># do validations
-</span>  <span class='kw'>begin</span>
-    <span class='id identifier rubyid_query_output'>query_output</span>                <span class='op'>=</span> <span class='const'>Output</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@filename</span><span class='comma'>,</span> <span class='ivar'>@html_path</span><span class='comma'>,</span> <span class='ivar'>@yaml_path</span><span class='comma'>,</span> <span class='ivar'>@idx</span><span class='comma'>,</span> <span class='ivar'>@start_idx</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_query_output'>query_output</span><span class='period'>.</span><span class='id identifier rubyid_prediction_len'>prediction_len</span> <span class='op'>=</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span>
-    <span class='id identifier rubyid_query_output'>query_output</span><span class='period'>.</span><span class='id identifier rubyid_prediction_def'>prediction_def</span> <span class='op'>=</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_definition'>definition</span>
-    <span class='id identifier rubyid_query_output'>query_output</span><span class='period'>.</span><span class='id identifier rubyid_nr_hits'>nr_hits</span>        <span class='op'>=</span> <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-    <span class='id identifier rubyid_plot_path'>plot_path</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_html_path'>html_path</span><span class='rbrace'>}</span><span class='tstring_content'>/</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_filename'>filename</span><span class='rbrace'>}</span><span class='tstring_content'>_</span><span class='embexpr_beg'>#{</span><span class='ivar'>@idx</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_validations'>validations</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-    <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>LengthClusterValidation</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@type</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='comma'>,</span> <span class='id identifier rubyid_plot_path'>plot_path</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>LengthRankValidation</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@type</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>BlastReadingFrameValidation</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@type</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>GeneMergeValidation</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@type</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='comma'>,</span> <span class='id identifier rubyid_plot_path'>plot_path</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>DuplicationValidation</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@type</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='comma'>,</span> <span class='ivar'>@mafft_path</span><span class='comma'>,</span> <span class='ivar'>@raw_seq_file_index</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>OpenReadingFrameValidation</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@type</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='comma'>,</span> <span class='id identifier rubyid_plot_path'>plot_path</span><span class='comma'>,</span> <span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>ATG</span><span class='tstring_end'>&quot;</span></span><span class='rbracket'>]</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>AlignmentValidation</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='ivar'>@type</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='comma'>,</span> <span class='id identifier rubyid_plot_path'>plot_path</span><span class='comma'>,</span> <span class='ivar'>@mafft_path</span><span class='comma'>,</span> <span class='ivar'>@raw_seq_file_index</span><span class='rparen'>)</span>
-    <span class='comment'># check the class type of the elements in the list
-</span>    <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
-      <span class='id identifier rubyid_raise'>raise</span> <span class='const'>ValidationClassError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>ValidationTest</span>
-    <span class='kw'>end</span>
-    <span class='comment'># check alias duplication
-</span>    <span class='kw'>unless</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_cli_name'>cli_name</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_cli_name'>cli_name</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-      <span class='id identifier rubyid_raise'>raise</span> <span class='const'>AliasDuplicationError</span>
-    <span class='kw'>end</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_vlist'>vlist</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_include?'>include?</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>all</span><span class='tstring_end'>&quot;</span></span>
-      <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_run'>run</span><span class='rbrace'>}</span>
-      <span class='comment'># check the class type of the validation reports
-</span>      <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
-        <span class='id identifier rubyid_raise'>raise</span> <span class='const'>ReportClassError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>ValidationReport</span>
-      <span class='kw'>end</span>
-      <span class='id identifier rubyid_query_output'>query_output</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_desired_validations'>desired_validations</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_vlist'>vlist</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_vv'>vv</span><span class='op'>|</span> <span class='id identifier rubyid_vv'>vv</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_include?'>include?</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_cli_name'>cli_name</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='rbrace'>}</span>
-      <span class='id identifier rubyid_desired_validations'>desired_validations</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
-          <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_run'>run</span>
-          <span class='id identifier rubyid_raise'>raise</span> <span class='const'>ReportClassError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>ValidationReport</span>
-      <span class='kw'>end</span>
-      <span class='id identifier rubyid_query_output'>query_output</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span> <span class='op'>=</span> <span class='id identifier rubyid_desired_validations'>desired_validations</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_query_output'>query_output</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>0</span>
-        <span class='id identifier rubyid_raise'>raise</span> <span class='const'>NoValidationError</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-  <span class='kw'>rescue</span> <span class='const'>ValidationClassError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Class Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: type of one of the validations is not ValidationTest\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit!'>exit!</span>
-  <span class='kw'>rescue</span> <span class='const'>NoValidationError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Validation error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: your -v arguments are not valid aliases\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit!'>exit!</span>
-  <span class='kw'>rescue</span> <span class='const'>ReportClassError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Class Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: type of one of the validation reports returned by the 'run' method is not ValidationReport\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit!'>exit!</span>
-  <span class='kw'>rescue</span> <span class='const'>AliasDuplicationError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Alias Duplication error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: At least two validations have the same CLI alias\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit!'>exit!</span>
-  <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>.\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit!'>exit!</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_query_output'>query_output</span><span class='period'>.</span><span class='id identifier rubyid_generate_html'>generate_html</span>
-  <span class='id identifier rubyid_query_output'>query_output</span><span class='period'>.</span><span class='id identifier rubyid_print_output_console'>print_output_console</span>
-  <span class='id identifier rubyid_query_output'>query_output</span><span class='period'>.</span><span class='id identifier rubyid_print_output_file_yaml'>print_output_file_yaml</span>
-  <span class='ivar'>@all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_query_output'>query_output</span><span class='rparen'>)</span>
-<span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-  <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>.\n</span><span class='tstring_end'>&quot;</span></span>
-  <span class='id identifier rubyid_exit'>exit</span>
-<span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="parse_output-instance_method">
-    - (<tt>Object</tt>) <strong>parse_output</strong>(output)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Parses the blast output: autodetect the format: xml or tabular  Param:
-<tt>output</tt>: <tt>String</tt> with the blast output</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 205</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_parse_output'>parse_output</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-    <span class='id identifier rubyid_iterator_xml'>iterator_xml</span> <span class='op'>=</span> <span class='const'>Bio</span><span class='op'>::</span><span class='const'>BlastXMLParser</span><span class='op'>::</span><span class='const'>NokogiriBlastXml</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_enum'>to_enum</span>
-    <span class='id identifier rubyid_iterator_tab'>iterator_tab</span> <span class='op'>=</span> <span class='const'>TabularParser</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='comma'>,</span> <span class='id identifier rubyid_tabular_format'>tabular_format</span><span class='comma'>,</span> <span class='ivar'>@type</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_input_file_type'>input_file_type</span> <span class='op'>=</span> <span class='symbol'>:xml</span>
-    <span class='kw'>begin</span>
-      <span class='comment'># get info about the query
-</span>      <span class='comment'># get the @idx-th sequence  from the fasta file
-</span>
-      <span class='id identifier rubyid_prediction'>prediction</span> <span class='op'>=</span> <span class='const'>Sequence</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-      <span class='kw'>if</span> <span class='ivar'>@idx</span><span class='op'>+</span><span class='int'>1</span> <span class='op'>==</span> <span class='ivar'>@query_offset_lst</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-        <span class='kw'>break</span>
-      <span class='kw'>end</span>
-      <span class='id identifier rubyid_query'>query</span>       <span class='op'>=</span> <span class='const'>IO</span><span class='period'>.</span><span class='id identifier rubyid_binread'>binread</span><span class='lparen'>(</span><span class='ivar'>@fasta_filepath</span><span class='comma'>,</span> <span class='ivar'>@query_offset_lst</span><span class='lbracket'>[</span><span class='ivar'>@idx</span><span class='op'>+</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='ivar'>@query_offset_lst</span><span class='lbracket'>[</span><span class='ivar'>@idx</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='ivar'>@query_offset_lst</span><span class='lbracket'>[</span><span class='ivar'>@idx</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-      <span class='id identifier rubyid_parse_query'>parse_query</span> <span class='op'>=</span> <span class='id identifier rubyid_query'>query</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>&gt;([^\n]*)\n([A-Za-z\n]*)</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
-      <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_definition'>definition</span>     <span class='op'>=</span> <span class='id identifier rubyid_parse_query'>parse_query</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-      <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_identifier'>identifier</span>     <span class='op'>=</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_definition'>definition</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'> .*</span><span class='regexp_end'>/</span></span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-      <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_type'>type</span>           <span class='op'>=</span> <span class='ivar'>@type</span>
-      <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span>   <span class='op'>=</span> <span class='id identifier rubyid_parse_query'>parse_query</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-      <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span> <span class='op'>=</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-      <span class='kw'>if</span> <span class='ivar'>@type</span> <span class='op'>==</span> <span class='symbol'>:nucleotide</span>
-        <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span> <span class='op'>/=</span> <span class='int'>3</span>
-      <span class='kw'>end</span>
-      <span class='ivar'>@idx</span> <span class='op'>=</span> <span class='ivar'>@idx</span> <span class='op'>+</span> <span class='int'>1</span>
-      <span class='kw'>begin</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_input_file_type'>input_file_type</span> <span class='op'>==</span> <span class='symbol'>:xml</span>
-          <span class='comment'># check xml format
-</span>          <span class='kw'>if</span> <span class='ivar'>@idx</span> <span class='op'>&lt;</span> <span class='ivar'>@start_idx</span>
-            <span class='id identifier rubyid_iter'>iter</span> <span class='op'>=</span> <span class='id identifier rubyid_iterator_xml'>iterator_xml</span><span class='period'>.</span><span class='id identifier rubyid_next'>next</span>
-          <span class='kw'>else</span>
-            <span class='id identifier rubyid_hits'>hits</span> <span class='op'>=</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_parse_next_query_xml'>parse_next_query_xml</span><span class='lparen'>(</span><span class='id identifier rubyid_iterator_xml'>iterator_xml</span><span class='comma'>,</span> <span class='ivar'>@type</span><span class='rparen'>)</span>
-            <span class='kw'>if</span> <span class='id identifier rubyid_hits'>hits</span> <span class='op'>==</span> <span class='kw'>nil</span>
-              <span class='ivar'>@idx</span> <span class='op'>=</span> <span class='ivar'>@idx</span> <span class='op'>-</span><span class='int'>1</span>
-              <span class='kw'>break</span>
-            <span class='kw'>end</span>
-            <span class='id identifier rubyid_do_validations'>do_validations</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='rparen'>)</span>
-          <span class='kw'>end</span>
-        <span class='kw'>else</span>
-          <span class='id identifier rubyid_raise'>raise</span> <span class='const'>Exception</span>
-        <span class='kw'>end</span>
-      <span class='kw'>rescue</span> <span class='const'>SequenceTypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-        <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Sequence Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-          <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: the blast output was not obtained against a protein database.\n</span><span class='tstring_end'>&quot;</span></span>
-        <span class='id identifier rubyid_exit!'>exit!</span>
-      <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-        <span class='kw'>begin</span>
-          <span class='id identifier rubyid_input_file_type'>input_file_type</span> <span class='op'>=</span> <span class='symbol'>:tabular</span>
-          <span class='kw'>if</span> <span class='ivar'>@tabular_format</span> <span class='op'>==</span> <span class='kw'>nil</span> <span class='kw'>and</span> <span class='ivar'>@xml_file</span><span class='op'>!=</span> <span class='kw'>nil</span>
-            <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Note: Please specify the --tabular argument if you used tabular format input with nonstandard columns.\n</span><span class='tstring_end'>&quot;</span></span>
-          <span class='kw'>end</span>
-          <span class='comment'>#check tabular format
-</span>          <span class='kw'>if</span> <span class='ivar'>@idx</span> <span class='op'>&lt;</span> <span class='ivar'>@start_idx</span>
-            <span class='id identifier rubyid_iterator_tab'>iterator_tab</span><span class='period'>.</span><span class='id identifier rubyid_jump_next'>jump_next</span>
-          <span class='kw'>else</span>
-            <span class='id identifier rubyid_hits'>hits</span> <span class='op'>=</span> <span class='id identifier rubyid_iterator_tab'>iterator_tab</span><span class='period'>.</span><span class='id identifier rubyid_next'>next</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_identifier'>identifier</span><span class='rparen'>)</span>
-            <span class='kw'>if</span> <span class='id identifier rubyid_hits'>hits</span> <span class='op'>==</span> <span class='kw'>nil</span>
-              <span class='ivar'>@idx</span> <span class='op'>=</span> <span class='ivar'>@idx</span> <span class='op'>-</span><span class='int'>1</span>
-              <span class='kw'>break</span>
-            <span class='kw'>end</span>
-            <span class='id identifier rubyid_do_validations'>do_validations</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='rparen'>)</span>
-          <span class='kw'>end</span>
-        <span class='kw'>rescue</span> <span class='const'>SequenceTypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-          <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Sequence Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-            <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: the blast output was not obtained against a protein database.\n</span><span class='tstring_end'>&quot;</span></span>
-          <span class='id identifier rubyid_exit!'>exit!</span>
-        <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-          <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Blast file error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-             <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: blast output file format is neihter xml nor tabular.\n</span><span class='tstring_end'>&quot;</span></span>
-          <span class='id identifier rubyid_exit!'>exit!</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span> <span class='kw'>while</span> <span class='int'>1</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="remove_identical_hits-instance_method">
-    - (<tt>Object</tt>) <strong>remove_identical_hits</strong>(prediction, hits)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Removes identical hits Params: <tt>prediction</tt>: Sequence object
-<tt>hits</tt>: Array of <tt>Sequence</tt> objects Output: new array of hit
-<tt>Sequence</tt> objects</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 291</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_remove_identical_hits'>remove_identical_hits</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='rparen'>)</span>
-  <span class='comment'># remove the identical hits
-</span>  <span class='comment'># identical hit means 100%coverage and &gt;99% identity
-</span>  <span class='id identifier rubyid_identical_hits'>identical_hits</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-  <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_hit'>hit</span><span class='op'>|</span>
-    <span class='comment'># check if all hsps have identity more than 99%
-</span>    <span class='id identifier rubyid_low_identity'>low_identity</span> <span class='op'>=</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_hsp_list'>hsp_list</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_hsp'>hsp</span><span class='op'>|</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_pidentity'>pidentity</span> <span class='op'>==</span> <span class='kw'>nil</span> <span class='kw'>or</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_pidentity'>pidentity</span> <span class='op'>&lt;</span> <span class='int'>99</span><span class='rbrace'>}</span>
-    <span class='comment'># check the coverage
-</span>    <span class='id identifier rubyid_coverage'>coverage</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span><span class='comma'>,</span><span class='int'>0</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_hsp_list'>hsp_list</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_hsp'>hsp</span><span class='op'>|</span>
-       <span class='id identifier rubyid_len'>len</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_to'>match_query_to</span> <span class='op'>-</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_from'>match_query_from</span> <span class='op'>+</span> <span class='int'>1</span>
-       <span class='id identifier rubyid_coverage'>coverage</span><span class='lbracket'>[</span><span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_from'>match_query_from</span><span class='op'>-</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_to'>match_query_to</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_len'>len</span><span class='comma'>,</span> <span class='int'>1</span><span class='rparen'>)</span>
-    <span class='kw'>end</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_low_identity'>low_identity</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>0</span> <span class='kw'>and</span> <span class='id identifier rubyid_coverage'>coverage</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>1</span>
-      <span class='id identifier rubyid_identical_hits'>identical_hits</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_hit'>hit</span><span class='rparen'>)</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_identical_hits'>identical_hits</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_hit'>hit</span><span class='op'>|</span> <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_delete'>delete</span><span class='lparen'>(</span><span class='id identifier rubyid_hit'>hit</span><span class='rparen'>)</span><span class='rbrace'>}</span>
-  <span class='kw'>return</span> <span class='id identifier rubyid_hits'>hits</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="validation-instance_method">
-    - (<tt>Object</tt>) <strong>validation</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Parse the blast output and run validations</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 151</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_validation'>validation</span>
-  <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nDepending on your input and your computational </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-       <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>resources, this may take a while. Please wait...</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>begin</span>
-    <span class='kw'>if</span> <span class='ivar'>@xml_file</span> <span class='op'>==</span> <span class='kw'>nil</span>
-      <span class='comment'>#file seek for each query
-</span>      <span class='ivar'>@query_offset_lst</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='ivar'>@query_offset_lst</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>2</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_pos'>pos</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
-        <span class='kw'>if</span> <span class='lparen'>(</span><span class='id identifier rubyid_i'>i</span><span class='op'>+</span><span class='int'>1</span><span class='rparen'>)</span> <span class='op'>&gt;=</span> <span class='ivar'>@start_idx</span>
-          <span class='id identifier rubyid_query'>query</span> <span class='op'>=</span> <span class='const'>IO</span><span class='period'>.</span><span class='id identifier rubyid_binread'>binread</span><span class='lparen'>(</span><span class='ivar'>@fasta_filepath</span><span class='comma'>,</span> <span class='ivar'>@query_offset_lst</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>+</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='ivar'>@query_offset_lst</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='ivar'>@query_offset_lst</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='semicolon'>;</span>
-          <span class='comment'>#call blast with the default parameters
-</span>          <span class='kw'>if</span> <span class='id identifier rubyid_type'>type</span> <span class='op'>==</span> <span class='symbol'>:protein</span>
-            <span class='id identifier rubyid_output'>output</span> <span class='op'>=</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_call_blast_from_stdin'>call_blast_from_stdin</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>blastp</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='id identifier rubyid_query'>query</span><span class='comma'>,</span> <span class='int'>11</span><span class='comma'>,</span> <span class='int'>1</span><span class='rparen'>)</span>
-          <span class='kw'>else</span>
-            <span class='id identifier rubyid_output'>output</span> <span class='op'>=</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_call_blast_from_stdin'>call_blast_from_stdin</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>blastx</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='id identifier rubyid_query'>query</span><span class='comma'>,</span> <span class='int'>11</span><span class='comma'>,</span> <span class='int'>1</span><span class='rparen'>)</span>
-          <span class='kw'>end</span>
-          <span class='comment'>#save output in a file
-</span>          <span class='comment'>#xml_file = &quot;blast/#{@fasta_filepath}_#{i+1}.xml&quot;
-</span>          <span class='comment'>#File.open(xml_file , &quot;w&quot;) do |f| f.write(output) end
-</span>
-          <span class='comment'>#parse output
-</span>          <span class='id identifier rubyid_parse_output'>parse_output</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='rparen'>)</span>
-        <span class='kw'>else</span>
-          <span class='ivar'>@idx</span> <span class='op'>=</span> <span class='ivar'>@idx</span> <span class='op'>+</span> <span class='int'>1</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_file'>file</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='ivar'>@xml_file</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>rb</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_read'>read</span>
-      <span class='comment'>#check the format of the input file
-</span>      <span class='id identifier rubyid_parse_output'>parse_output</span><span class='lparen'>(</span><span class='id identifier rubyid_file'>file</span><span class='rparen'>)</span>
-    <span class='kw'>end</span>
-    <span class='const'>Output</span><span class='period'>.</span><span class='id identifier rubyid_print_footer'>print_footer</span><span class='lparen'>(</span><span class='ivar'>@all_query_outputs</span><span class='comma'>,</span> <span class='ivar'>@html_path</span><span class='rparen'>)</span>
-  <span class='kw'>rescue</span> <span class='const'>SystemCallError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Load error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: input file is not valid\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit'>exit</span>
-  <span class='kw'>rescue</span> <span class='const'>SequenceTypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Sequence Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: the blast output was not obtained against a protein database.\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit!'>exit!</span>
-  <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-     <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>.\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit!'>exit!</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="which-instance_method">
-    - (<tt>Object</tt>) <strong>which</strong>(cmd)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>The ruby equivalent for 'which' command in unix</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation.rb', line 409</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_which'>which</span><span class='lparen'>(</span><span class='id identifier rubyid_cmd'>cmd</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_exts'>exts</span> <span class='op'>=</span> <span class='const'>ENV</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>PATHEXT</span><span class='tstring_end'>'</span></span><span class='rbracket'>]</span> <span class='op'>?</span> <span class='const'>ENV</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>PATHEXT</span><span class='tstring_end'>'</span></span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>;</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='op'>:</span> <span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_end'>'</span></span><span class='rbracket'>]</span>
-  <span class='const'>ENV</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>PATH</span><span class='tstring_end'>'</span></span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='const'>File</span><span class='op'>::</span><span class='const'>PATH_SEPARATOR</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_path'>path</span><span class='op'>|</span>
-    <span class='id identifier rubyid_exts'>exts</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_ext'>ext</span><span class='op'>|</span>
-      <span class='id identifier rubyid_exe'>exe</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='id identifier rubyid_path'>path</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_cmd'>cmd</span><span class='rbrace'>}</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_ext'>ext</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-      <span class='kw'>return</span> <span class='id identifier rubyid_exe'>exe</span> <span class='kw'>if</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_executable?'>executable?</span> <span class='id identifier rubyid_exe'>exe</span>
-    <span class='rbrace'>}</span>
-  <span class='kw'>end</span>
-  <span class='kw'>return</span> <span class='kw'>nil</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
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-</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).
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