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

genevalidator 1.6.1 → 1.6.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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

data/doc/Validation.html DELETED

@@ -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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-147</pre>
-    </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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