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

genevalidator 1.6.1 → 1.6.2

Files changed (131) hide show

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

data/doc/BlastReadingFrameValidation.html DELETED

@@ -1,370 +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: BlastReadingFrameValidation
-    &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 (B)</a> &raquo;
-    <span class="title">BlastReadingFrameValidation</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: BlastReadingFrameValidation
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName"><span class='object_link'><a href="ValidationTest.html" title="ValidationTest (class)">ValidationTest</a></span></span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next"><span class='object_link'><a href="ValidationTest.html" title="ValidationTest (class)">ValidationTest</a></span></li>
-            <li class="next">BlastReadingFrameValidation</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/validation_blast_reading_frame.rb</dd>
-</dl>
-<div class="clear"></div>
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-<p>This class contains the methods necessary for  reading frame validation
-based on BLAST output</p>
-  </div>
-</div>
-<div class="tags">
-</div>
-  <h2>Instance Attribute Summary</h2>
-  <h3 class="inherited">Attributes inherited from <span class='object_link'><a href="ValidationTest.html" title="ValidationTest (class)">ValidationTest</a></span></h3>
-  <p class="inherited"><span class='object_link'><a href="ValidationTest.html#cli_name-instance_method" title="ValidationTest#cli_name (method)">#cli_name</a></span>, <span class='object_link'><a href="ValidationTest.html#description-instance_method" title="ValidationTest#description (method)">#description</a></span>, <span class='object_link'><a href="ValidationTest.html#header-instance_method" title="ValidationTest#header (method)">#header</a></span>, <span class='object_link'><a href="ValidationTest.html#hits-instance_method" title="ValidationTest#hits (method)">#hits</a></span>, <span class='object_link'><a href="ValidationTest.html#prediction-instance_method" title="ValidationTest#prediction (method)">#prediction</a></span>, <span class='object_link'><a href="ValidationTest.html#running_time-instance_method" title="ValidationTest#running_time (method)">#running_time</a></span>, <span class='object_link'><a href="ValidationTest.html#short_header-instance_method" title="ValidationTest#short_header (method)">#short_header</a></span>, <span class='object_link'><a href="ValidationTest.html#type-instance_method" title="ValidationTest#type (method)">#type</a></span>, <span class='object_link'><a href="ValidationTest.html#validation_report-instance_method" title="ValidationTest#validation_report (method)">#validation_report</a></span></p>
-    <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="#initialize-instance_method" title="#initialize (instance method)">- (BlastReadingFrameValidation) <strong>initialize</strong>(type, prediction, hits = nil) </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>A new instance of BlastReadingFrameValidation.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#run-instance_method" title="#run (instance method)">- (Object) <strong>run</strong>(lst = @hits) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Check reading frame inconsistency Params: <tt>lst</tt>: vector of
-<tt>Sequence</tt> objects Output: <tt>BlastRFValidationOutput</tt> object.</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="BlastReadingFrameValidation (class)">BlastReadingFrameValidation</a></span></tt>) <strong>initialize</strong>(type, prediction, hits = nil)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns a new instance of BlastReadingFrameValidation</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_blast_reading_frame.rb', line 53</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_type'>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='op'>=</span> <span class='kw'>nil</span><span class='rparen'>)</span>
-  <span class='kw'>super</span>
-  <span class='ivar'>@short_header</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Frame</span><span class='tstring_end'>&quot;</span></span>
-  <span class='ivar'>@header</span>       <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Reading Frame</span><span class='tstring_end'>&quot;</span></span>
-  <span class='ivar'>@description</span>  <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Check whether there is a single reading frame among BLAST</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'> hits. Otherwise there might be a reading frame shift in the query sequence.</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'> Meaning of the output displayed: (reading frame: no hsps)</span><span class='tstring_end'>&quot;</span></span>
-  <span class='ivar'>@cli_name</span>     <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>frame</span><span class='tstring_end'>&quot;</span></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="run-instance_method">
-    - (<tt>Object</tt>) <strong>run</strong>(lst = @hits)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Check reading frame inconsistency Params: <tt>lst</tt>: vector of
-<tt>Sequence</tt> objects Output: <tt>BlastRFValidationOutput</tt> object</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_blast_reading_frame.rb', line 69</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_run'>run</span><span class='lparen'>(</span><span class='id identifier rubyid_lst'>lst</span> <span class='op'>=</span> <span class='ivar'>@hits</span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_type'>type</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span> <span class='op'>!=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>nucleotide</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:unapplicable</span><span class='rparen'>)</span>
-      <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>NotEnoughHitsError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>&gt;=</span> <span class='int'>5</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>Exception</span> <span class='kw'>unless</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span> <span class='kw'>and</span> <span class='id identifier rubyid_hits'>hits</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span>
-    <span class='id identifier rubyid_start'>start</span> <span class='op'>=</span> <span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span>
-    <span class='id identifier rubyid_rfs'>rfs</span> <span class='op'>=</span>  <span class='id identifier rubyid_lst'>lst</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_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span><span class='period'>.</span><span class='id identifier rubyid_hsp_list'>hsp_list</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_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span><span class='period'>.</span><span class='id identifier rubyid_query_reading_frame'>query_reading_frame</span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-    <span class='id identifier rubyid_frames_histo'>frames_histo</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='id identifier rubyid_rfs'>rfs</span><span class='period'>.</span><span class='id identifier rubyid_group_by'>group_by</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span> <span class='rbrace'>}</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_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_vs'>vs</span><span class='op'>|</span> <span class='lbracket'>[</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_vs'>vs</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span> <span class='rbrace'>}</span><span class='rbracket'>]</span>
-    <span class='comment'># get the main reading frame
-</span>    <span class='id identifier rubyid_main_rf'>main_rf</span> <span class='op'>=</span> <span class='id identifier rubyid_frames_histo'>frames_histo</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_k'>k</span><span class='comma'>,</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_max'>max</span>
-    <span class='ivar'>@prediction</span><span class='period'>.</span><span class='id identifier rubyid_nucleotide_rf'>nucleotide_rf</span> <span class='op'>=</span> <span class='id identifier rubyid_frames_histo'>frames_histo</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_k'>k</span><span class='comma'>,</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='op'>==</span><span class='id identifier rubyid_main_rf'>main_rf</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span>
-    <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>BlastRFValidationOutput</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_frames_histo'>frames_histo</span><span class='rparen'>)</span>
-    <span class='ivar'>@running_time</span> <span class='op'>=</span> <span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span> <span class='op'>-</span> <span class='id identifier rubyid_start'>start</span>
-    <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-  <span class='comment'># Exception is raised when blast founds no hits
-</span>  <span class='kw'>rescue</span>  <span class='const'>NotEnoughHitsError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Not enough evidence</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:warning</span><span class='rparen'>)</span>
-    <span class='kw'>return</span> <span class='ivar'>@validation_report</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='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Unexpected error</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:error</span><span class='rparen'>)</span>
-    <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Sat Sep 28 07:01:33 2013 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.2 (ruby-1.9.3).
-</div>
-  </body>
-</html>

data/doc/BlastUtils.html DELETED

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-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Class: BlastUtils
-    &mdash; Documentation by YARD 0.8.7.2
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-    <div id="header">
-      <div id="menu">
-    <a href="_index.html">Index (B)</a> &raquo;
-    <span class="title">BlastUtils</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>
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-        href="method_list.html">
-      Method List
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-        href="file_list.html">
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-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: BlastUtils
-</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">BlastUtils</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/blast.rb</dd>
-</dl>
-<div class="clear"></div>
-    <h2>
-      Class Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#call_blast_from_file-class_method" title="call_blast_from_file (class method)">+ (Object) <strong>call_blast_from_file</strong>(command, filename, gapopen, gapextend, db = &quot;nr -remote&quot;) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Calls blast from file with specific parameters Param: <tt>command</tt>:
-blast command in String format (e.g 'blastx' or 'blastp')
-<tt>filename</tt>: name of the FAST file <tt>query</tt>: <tt>String</tt>
-containing the the query in fasta format <tt>gapopen</tt>: gapopen blast
-parameter <tt>gapextend</tt>: gapextend blast parameter <tt>db</tt>:
-database Output: String with the blast xml output.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#call_blast_from_stdin-class_method" title="call_blast_from_stdin (class method)">+ (Object) <strong>call_blast_from_stdin</strong>(command, query, gapopen, gapextend, db = &quot;nr -remote&quot;) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Calls blast from standard input with specific parameters Params:
-<tt>command</tt>: blast command in String format (e.g 'blastx' or 'blastp')
-<tt>query</tt>: String containing the the query in fasta format
-<tt>gapopen</tt>: gapopen blast parameter <tt>gapextend</tt>: gapextend
-blast parameter <tt>db</tt>: database Output: String with the blast xml
-output.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#composition-class_method" title="composition (class method)">+ (Object) <strong>composition</strong>(sequence_string) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Method copied from sequenceserver/sequencehelpers.rb Params:
-sequence_string: String of which we mfind the composition Output: a Hash.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#guess_sequence_type-class_method" title="guess_sequence_type (class method)">+ (Object) <strong>guess_sequence_type</strong>(sequence_string) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Method copied from sequenceserver/sequencehelpers.rb Strips all non-letter
-characters.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#parse_next_query_xml-class_method" title="parse_next_query_xml (class method)">+ (Object) <strong>parse_next_query_xml</strong>(iterator, type) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Parses the next query from the blast xml output query Params:
-<tt>iterator</tt>: blast xml iterator for hits <tt>type</tt>: the type of
-the sequence: :nucleotide or :protein Outputs: Array of <tt>Sequence</tt>
-ojbects for hits.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#type_of_sequences-class_method" title="type_of_sequences (class method)">+ (Object) <strong>type_of_sequences</strong>(fasta_format_string) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Method copied from sequenceserver/sequencehelpers.rb Splits input at
-putative fasta definition lines (like "&gt;adsfadsf"), guesses sequence
-type for each sequence.</p>
-</div></span>
-</li>
-    </ul>
-  <div id="class_method_details" class="method_details_list">
-    <h2>Class Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="call_blast_from_file-class_method">
-    + (<tt>Object</tt>) <strong>call_blast_from_file</strong>(command, filename, gapopen, gapextend, db = &quot;nr -remote&quot;)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Calls blast from file with specific parameters Param: <tt>command</tt>:
-blast command in String format (e.g 'blastx' or 'blastp')
-<tt>filename</tt>: name of the FAST file <tt>query</tt>: <tt>String</tt>
-containing the the query in fasta format <tt>gapopen</tt>: gapopen blast
-parameter <tt>gapextend</tt>: gapextend blast parameter <tt>db</tt>:
-database Output: String with the blast xml 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/blast.rb', line 66</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_call_blast_from_file'>call_blast_from_file</span><span class='lparen'>(</span><span class='id identifier rubyid_command'>command</span><span class='comma'>,</span> <span class='id identifier rubyid_filename'>filename</span><span class='comma'>,</span> <span class='id identifier rubyid_gapopen'>gapopen</span><span class='comma'>,</span> <span class='id identifier rubyid_gapextend'>gapextend</span><span class='comma'>,</span> <span class='id identifier rubyid_db'>db</span><span class='op'>=</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>nr -remote</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>TypeError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_command'>command</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>String</span> <span class='kw'>and</span> <span class='id identifier rubyid_filename'>filename</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>String</span>
-    <span class='id identifier rubyid_evalue'>evalue</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>1e-5</span><span class='tstring_end'>&quot;</span></span>
-    <span class='comment'>#output = 5 (XML Blast output)
-</span>    <span class='id identifier rubyid_cmd'>cmd</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_command'>command</span><span class='rbrace'>}</span><span class='tstring_content'> -query </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_filename'>filename</span><span class='rbrace'>}</span><span class='tstring_content'> -db </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_db'>db</span><span class='rbrace'>}</span><span class='tstring_content'> -evalue </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_evalue'>evalue</span><span class='rbrace'>}</span><span class='tstring_content'> -outfmt 5 -gapopen </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gapopen'>gapopen</span><span class='rbrace'>}</span><span class='tstring_content'> -gapextend </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gapextend'>gapextend</span><span class='rbrace'>}</span><span class='tstring_content'> </span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Executing \&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_cmd'>cmd</span><span class='rbrace'>}</span><span class='tstring_content'>\&quot;...</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>This may take a while...</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_output'>output</span> <span class='op'>=</span> <span class='backtick'>%x[</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_cmd'>cmd</span><span class='rbrace'>}</span><span class='tstring_content'>          if xml_file == nil
-          file = File.open(xml_file, &quot;rb&quot;).read
-          b.parse_xml_output(file)
-        end 2&gt;/dev/null</span><span class='tstring_end'>]</span></span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_output'>output</span><span class='period'>.</span><span class='id identifier rubyid_empty?'>empty?</span>
-      <span class='id identifier rubyid_raise'>raise</span> <span class='const'>ClasspathError</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='kw'>end</span>
-    <span class='kw'>return</span> <span class='id identifier rubyid_output'>output</span>
-  <span class='kw'>rescue</span> <span class='const'>TypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: one of the arguments of 'call_blast_from_file' method has not the proper type\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit'>exit</span>
-  <span class='kw'>rescue</span> <span class='const'>ClasspathError</span> <span class='op'>=&gt;</span><span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$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 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'>Did you add BLAST path to LOADPATH?\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="call_blast_from_stdin-class_method">
-    + (<tt>Object</tt>) <strong>call_blast_from_stdin</strong>(command, query, gapopen, gapextend, db = &quot;nr -remote&quot;)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Calls blast from standard input with specific parameters Params:
-<tt>command</tt>: blast command in String format (e.g 'blastx' or 'blastp')
-<tt>query</tt>: String containing the the query in fasta format
-<tt>gapopen</tt>: gapopen blast parameter <tt>gapextend</tt>: gapextend
-blast parameter <tt>db</tt>: database Output: String with the blast xml
-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/blast.rb', line 26</span>
-<span class='kw'>def</span> <span class='kw'>self</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='id identifier rubyid_command'>command</span><span class='comma'>,</span> <span class='id identifier rubyid_query'>query</span><span class='comma'>,</span> <span class='id identifier rubyid_gapopen'>gapopen</span><span class='comma'>,</span> <span class='id identifier rubyid_gapextend'>gapextend</span><span class='comma'>,</span> <span class='id identifier rubyid_db'>db</span><span class='op'>=</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>nr -remote</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>TypeError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_command'>command</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>String</span> <span class='kw'>and</span> <span class='id identifier rubyid_query'>query</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>String</span>
-    <span class='id identifier rubyid_evalue'>evalue</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>1e-5</span><span class='tstring_end'>&quot;</span></span>
-    <span class='comment'>#output format = 5 (XML Blast output)
-</span>    <span class='id identifier rubyid_blast_cmd'>blast_cmd</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_command'>command</span><span class='rbrace'>}</span><span class='tstring_content'> -db </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_db'>db</span><span class='rbrace'>}</span><span class='tstring_content'> -evalue </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_evalue'>evalue</span><span class='rbrace'>}</span><span class='tstring_content'> -outfmt 5 -gapopen </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gapopen'>gapopen</span><span class='rbrace'>}</span><span class='tstring_content'> -gapextend </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gapextend'>gapextend</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_cmd'>cmd</span>       <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>echo \&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_query'>query</span><span class='rbrace'>}</span><span class='tstring_content'>\&quot; | </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_blast_cmd'>blast_cmd</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_output'>output</span>    <span class='op'>=</span> <span class='backtick'>%x[</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_cmd'>cmd</span><span class='rbrace'>}</span><span class='tstring_content'> 2&gt;/dev/null</span><span class='tstring_end'>]</span></span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_output'>output</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
-      <span class='id identifier rubyid_raise'>raise</span> <span class='const'>ClasspathError</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='kw'>end</span>
-    <span class='kw'>return</span> <span class='id identifier rubyid_output'>output</span>
-  <span class='kw'>rescue</span> <span class='const'>TypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: one of the arguments of 'call_blast_from_file' method has not the proper type\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit'>exit</span>
-  <span class='kw'>rescue</span> <span class='const'>ClasspathError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$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 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 installation path is not in the LOAD PATH.\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="composition-class_method">
-    + (<tt>Object</tt>) <strong>composition</strong>(sequence_string)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Method copied from sequenceserver/sequencehelpers.rb Params:
-sequence_string: String of which we mfind the composition Output: a Hash</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/blast.rb', line 185</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_composition'>composition</span><span class='lparen'>(</span><span class='id identifier rubyid_sequence_string'>sequence_string</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_count'>count</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_sequence_string'>sequence_string</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'>.</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span>
-    <span class='id identifier rubyid_count'>count</span><span class='lbracket'>[</span><span class='id identifier rubyid_x'>x</span><span class='rbracket'>]</span> <span class='op'>+=</span> <span class='int'>1</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_count'>count</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="guess_sequence_type-class_method">
-    + (<tt>Object</tt>) <strong>guess_sequence_type</strong>(sequence_string)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Method copied from sequenceserver/sequencehelpers.rb Strips all non-letter
-characters. guestimates sequence based on that. If less than 10 useable
-characters... returns nil If more than 90% ACGTU returns :nucleotide. else
-returns :protein Params: <tt>sequence_string</tt>: String to validate
-Output: nil, :nucleotide or :protein</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/blast.rb', line 202</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_guess_sequence_type'>guess_sequence_type</span><span class='lparen'>(</span><span class='id identifier rubyid_sequence_string'>sequence_string</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_cleaned_sequence'>cleaned_sequence</span> <span class='op'>=</span> <span class='id identifier rubyid_sequence_string'>sequence_string</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'>[^A-Z]</span><span class='regexp_end'>/i</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='comment'># removing non-letter characters
-</span>  <span class='id identifier rubyid_cleaned_sequence'>cleaned_sequence</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'>[NX]</span><span class='regexp_end'>/i</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='comment'># removing ambiguous characters
-</span>
-  <span class='kw'>return</span> <span class='kw'>nil</span> <span class='kw'>if</span> <span class='id identifier rubyid_cleaned_sequence'>cleaned_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>&lt;</span> <span class='int'>10</span> <span class='comment'># conservative
-</span>
-  <span class='id identifier rubyid_composition'>composition</span> <span class='op'>=</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_composition'>composition</span><span class='lparen'>(</span><span class='id identifier rubyid_cleaned_sequence'>cleaned_sequence</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_composition_NAs'>composition_NAs</span> <span class='op'>=</span> <span class='id identifier rubyid_composition'>composition</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_character'>character</span><span class='comma'>,</span> <span class='id identifier rubyid_count'>count</span><span class='op'>|</span><span class='id identifier rubyid_character'>character</span><span class='period'>.</span><span class='id identifier rubyid_match'>match</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>[ACGTU]</span><span class='regexp_end'>/i</span></span><span class='rparen'>)</span> <span class='rbrace'>}</span> <span class='comment'># only putative NAs
-</span>  <span class='id identifier rubyid_putative_NA_counts'>putative_NA_counts</span> <span class='op'>=</span> <span class='id identifier rubyid_composition_NAs'>composition_NAs</span><span class='period'>.</span><span class='id identifier rubyid_collect'>collect</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_key_value_array'>key_value_array</span><span class='op'>|</span> <span class='id identifier rubyid_key_value_array'>key_value_array</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='rbrace'>}</span> <span class='comment'># only count, not char
-</span>  <span class='id identifier rubyid_putative_NA_sum'>putative_NA_sum</span> <span class='op'>=</span> <span class='id identifier rubyid_putative_NA_counts'>putative_NA_counts</span><span class='period'>.</span><span class='id identifier rubyid_inject'>inject</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_sum'>sum</span><span class='comma'>,</span> <span class='id identifier rubyid_n'>n</span><span class='op'>|</span> <span class='id identifier rubyid_sum'>sum</span> <span class='op'>+</span> <span class='id identifier rubyid_n'>n</span> <span class='rbrace'>}</span> <span class='comment'># count of all putative NA
-</span>  <span class='id identifier rubyid_putative_NA_sum'>putative_NA_sum</span> <span class='op'>=</span> <span class='int'>0</span> <span class='kw'>if</span> <span class='id identifier rubyid_putative_NA_sum'>putative_NA_sum</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_putative_NA_sum'>putative_NA_sum</span> <span class='op'>&gt;</span> <span class='lparen'>(</span><span class='float'>0.9</span> <span class='op'>*</span> <span class='id identifier rubyid_cleaned_sequence'>cleaned_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rparen'>)</span>
-    <span class='kw'>return</span> <span class='symbol'>:nucleotide</span>
-  <span class='kw'>else</span>
-    <span class='kw'>return</span> <span class='symbol'>:protein</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_next_query_xml-class_method">
-    + (<tt>Object</tt>) <strong>parse_next_query_xml</strong>(iterator, type)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Parses the next query from the blast xml output query Params:
-<tt>iterator</tt>: blast xml iterator for hits <tt>type</tt>: the type of
-the sequence: :nucleotide or :protein Outputs: Array of <tt>Sequence</tt>
-ojbects for hits</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/blast.rb', line 105</span>
-<span class='kw'>def</span> <span class='kw'>self</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'>iterator</span><span class='comma'>,</span> <span class='id identifier rubyid_type'>type</span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>TypeError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_iterator'>iterator</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Enumerator</span>
-    <span class='id identifier rubyid_hits'>hits</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='id identifier rubyid_predicted_seq'>predicted_seq</span> <span class='op'>=</span> <span class='const'>Sequence</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='id identifier rubyid_iter'>iter</span> <span class='op'>=</span> <span class='id identifier rubyid_iterator'>iterator</span><span class='period'>.</span><span class='id identifier rubyid_next'>next</span>
-    <span class='comment'># parse blast the xml output and get the hits
-</span>    <span class='comment'># hits obtained are proteins! (we use only blastp and blastx)
-</span>    <span class='id identifier rubyid_iter'>iter</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='id identifier rubyid_seq'>seq</span> <span class='op'>=</span> <span class='const'>Sequence</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span> <span class='op'>=</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_len'>len</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_type'>type</span>           <span class='op'>=</span> <span class='symbol'>:protein</span>
-      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_identifier'>identifier</span>     <span class='op'>=</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_hit_id'>hit_id</span>
-      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_definition'>definition</span>     <span class='op'>=</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_hit_def'>hit_def</span>
-      <span class='comment'>#puts seq.identifier
-</span>      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_accession_no'>accession_no</span> <span class='op'>=</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_accession'>accession</span>
-      <span class='comment'># get all high-scoring segment pairs (hsp)
-</span>      <span class='id identifier rubyid_hsps'>hsps</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-      <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_hsps'>hsps</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_current_hsp'>current_hsp</span>            <span class='op'>=</span> <span class='const'>Hsp</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_hsp_evalue'>hsp_evalue</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_evalue'>evalue</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_from'>hit_from</span>         <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_from'>hit_from</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_to'>hit_to</span>           <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_to'>hit_to</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_from'>match_query_from</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_from'>query_from</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_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_query_to'>query_to</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_type'>type</span> <span class='op'>==</span> <span class='symbol'>:nucleotide</span>
-          <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_from'>match_query_from</span> <span class='op'>=</span>  <span class='lparen'>(</span><span class='id identifier rubyid_current_hsp'>current_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'>3</span><span class='rparen'>)</span> <span class='op'>+</span> <span class='int'>1</span>
-          <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_to'>match_query_to</span>   <span class='op'>=</span>  <span class='lparen'>(</span><span class='id identifier rubyid_current_hsp'>current_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'>3</span><span class='rparen'>)</span> <span class='op'>+</span> <span class='int'>1</span>
-        <span class='kw'>end</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_reading_frame'>query_reading_frame</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_frame'>query_frame</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_alignment'>hit_alignment</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_hseq'>hseq</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span>
-        <span class='kw'>if</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_guess_sequence_type'>guess_sequence_type</span><span class='lparen'>(</span><span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_alignment'>hit_alignment</span><span class='rparen'>)</span> <span class='op'>!=</span> <span class='symbol'>:protein</span>
-          <span class='id identifier rubyid_raise'>raise</span> <span class='const'>SequenceTypeError</span>
-        <span class='kw'>end</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_alignment'>query_alignment</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_qseq'>qseq</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span>
-        <span class='kw'>if</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_guess_sequence_type'>guess_sequence_type</span><span class='lparen'>(</span><span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_alignment'>query_alignment</span><span class='rparen'>)</span> <span class='op'>!=</span> <span class='symbol'>:protein</span>
-          <span class='id identifier rubyid_raise'>raise</span> <span class='const'>SequenceTypeError</span>
-        <span class='kw'>end</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_align_len'>align_len</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_align_len'>align_len</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_identity'>identity</span>  <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_identity'>identity</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_pidentity'>pidentity</span> <span class='op'>=</span> <span class='int'>100</span> <span class='op'>*</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_identity'>identity</span> <span class='op'>/</span> <span class='lparen'>(</span><span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_align_len'>align_len</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
-        <span class='id identifier rubyid_hsps'>hsps</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='rparen'>)</span>
-      <span class='kw'>end</span>
-      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_hsp_list'>hsp_list</span> <span class='op'>=</span> <span class='id identifier rubyid_hsps'>hsps</span>
-      <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_seq'>seq</span><span class='rparen'>)</span>
-    <span class='kw'>end</span>
-    <span class='kw'>return</span> <span class='id identifier rubyid_hits'>hits</span>
-  <span class='kw'>rescue</span> <span class='const'>TypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: you didn't call parse method first!\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit!'>exit!</span>
-  <span class='kw'>rescue</span> <span class='const'>SequenceTypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$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'>StopIteration</span>
-    <span class='kw'>nil</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="type_of_sequences-class_method">
-    + (<tt>Object</tt>) <strong>type_of_sequences</strong>(fasta_format_string)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Method copied from sequenceserver/sequencehelpers.rb Splits input at
-putative fasta definition lines (like "&gt;adsfadsf"), guesses sequence
-type for each sequence. If not enough sequence to determine, returns nil.
-If 2 kinds of sequence mixed together, raises ArgumentError Otherwise,
-returns :nucleotide or :protein Params: <tt>sequence_string</tt>: String to
-validate Output: nil, :nucleotide or :protein</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/blast.rb', line 231</span>
-<span class='kw'>def</span> <span class='kw'>self</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_format_string'>fasta_format_string</span><span class='rparen'>)</span>
-  <span class='comment'># the first sequence does not need to have a fasta definition line
-</span>  <span class='id identifier rubyid_sequences'>sequences</span> <span class='op'>=</span> <span class='id identifier rubyid_fasta_format_string'>fasta_format_string</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'>^&gt;.*$</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_delete_if'>delete_if</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_seq'>seq</span><span class='op'>|</span> <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_empty?'>empty?</span> <span class='rbrace'>}</span>
-  <span class='comment'># get all sequence types
-</span>  <span class='id identifier rubyid_sequence_types'>sequence_types</span> <span class='op'>=</span> <span class='id identifier rubyid_sequences'>sequences</span><span class='period'>.</span><span class='id identifier rubyid_collect'>collect</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_seq'>seq</span><span class='op'>|</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_guess_sequence_type'>guess_sequence_type</span><span class='lparen'>(</span><span class='id identifier rubyid_seq'>seq</span><span class='rparen'>)</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_compact'>compact</span>
-  <span class='kw'>return</span> <span class='kw'>nil</span> <span class='kw'>if</span> <span class='id identifier rubyid_sequence_types'>sequence_types</span><span class='period'>.</span><span class='id identifier rubyid_empty?'>empty?</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_sequence_types'>sequence_types</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>1</span>
-    <span class='kw'>return</span> <span class='id identifier rubyid_sequence_types'>sequence_types</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span> <span class='comment'># there is only one (but yes its an array)
-</span>  <span class='kw'>else</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>SequenceTypeError</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Sat Sep 28 07:01:32 2013 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.2 (ruby-1.9.3).
-</div>
-  </body>
-</html>