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/Blast.html DELETED

@@ -1,1905 +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: Blast
-    &mdash; Documentation by YARD 0.8.7
-</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">Blast</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: Blast
-</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">Blast</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>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="#fasta_file-instance_method" title="#fasta_file (instance method)">- (Object) <strong>fasta_file</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute fasta_file.</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="note title readonly">readonly</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="#outfmt-instance_method" title="#outfmt (instance method)">- (Object) <strong>outfmt</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute outfmt.</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="#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="#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>
-  </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="#blast-instance_method" title="#blast (instance method)">- (Object) <strong>blast</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Calls blast according to the type of the sequence.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#call_blast_from_file-instance_method" title="#call_blast_from_file (instance method)">- (Object) <strong>call_blast_from_file</strong>(command, filename, gapopen, gapextend) </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 Output: String with
-the blast xml output.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#call_blast_from_stdin-instance_method" title="#call_blast_from_stdin (instance method)">- (Object) <strong>call_blast_from_stdin</strong>(command, query, gapopen, gapextend) </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 Output: String with the blast xml output.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#composition-instance_method" title="#composition (instance 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="#get_sequence_by_accession_no-instance_method" title="#get_sequence_by_accession_no (instance method)">- (Object) <strong>get_sequence_by_accession_no</strong>(accno, db) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Gets gene by accession number from a givem database Params: <tt>accno</tt>:
-accession number as String <tt>db</tt>: database as String Output: String
-with the nucleotide sequence corresponding to the accno.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#guess_sequence_type-instance_method" title="#guess_sequence_type (instance 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="#initialize-instance_method" title="#initialize (instance method)">- (Blast) <strong>initialize</strong>(fasta_file, type, xml_file = nil, outfmt = 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_file</tt>: query sequence fasta
-file with query sequences <tt>type</tt>: query sequence type; can be
-:nucleotide or :protein <tt>xml_file</tt>: name of the precalculated blast
-xml output (used in 'skip blast' case) <tt>outfmt</tt>: output format
-<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_next_query-instance_method" title="#parse_next_query (instance method)">- (Object) <strong>parse_next_query</strong>(iterator) </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 Outputs: output1: an array
-of <tt>Sequence</tt> ojbects for hits output2: <tt>Sequence</tt> object for
-the predicted sequence.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#parse_xml_output-instance_method" title="#parse_xml_output (instance method)">- (Object) <strong>parse_xml_output</strong>(output) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Parses the xml blast output  Param: <tt>output</tt>: <tt>String</tt> with
-the blast output in xml format.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#type_of_sequences-instance_method" title="#type_of_sequences (instance 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="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="Blast (class)">Blast</a></span></tt>) <strong>initialize</strong>(fasta_file, type, xml_file = nil, outfmt = nil, start_idx = 1)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Initilizes the object Params: <tt>fasta_file</tt>: query sequence fasta
-file with query sequences <tt>type</tt>: query sequence type; can be
-:nucleotide or :protein <tt>xml_file</tt>: name of the precalculated blast
-xml output (used in 'skip blast' case) <tt>outfmt</tt>: output format
-<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">
-35
-36
-37
-38
-39
-40
-41
-42
-43
-44
-45
-46
-47
-48
-49
-50
-51
-52
-53
-54
-55
-56
-57
-58
-59
-60
-61
-62
-63
-64
-65
-66
-67
-68
-69
-70
-71
-72
-73
-74
-75</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 35</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_fasta_file'>fasta_file</span><span class='comma'>,</span> <span class='id identifier rubyid_type'>type</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_outfmt'>outfmt</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='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 resources, this may take a while. Please wait...\n\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_type'>type</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>protein</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@type</span> <span class='op'>=</span> <span class='symbol'>:protein</span>
-    <span class='kw'>else</span>
-      <span class='ivar'>@type</span> <span class='op'>=</span> <span class='symbol'>:nucleotide</span>
-    <span class='kw'>end</span>
-    <span class='ivar'>@fasta_file</span> <span class='op'>=</span> <span class='id identifier rubyid_fasta_file'>fasta_file</span>
-    <span class='ivar'>@xml_file</span> <span class='op'>=</span> <span class='id identifier rubyid_xml_file'>xml_file</span>
-    <span class='ivar'>@idx</span> <span class='op'>=</span> <span class='int'>0</span>
-    <span class='ivar'>@start_idx</span> <span class='op'>=</span> <span class='id identifier rubyid_start_idx'>start_idx</span>
-    <span class='ivar'>@outfmt</span> <span class='op'>=</span> <span class='id identifier rubyid_outfmt'>outfmt</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_file</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_file</span><span class='rparen'>)</span><span class='semicolon'>;</span>
-    <span class='comment'># type validation: the type of the sequence in the FASTA correspond to the one declared by the user
-</span>    <span class='kw'>if</span> <span class='ivar'>@type</span> <span class='op'>!=</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='id identifier rubyid_raise'>raise</span> <span class='const'>SequenceTypeError</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='kw'>end</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='comment'># redirect the cosole messages of R
-</span>    <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_echo'>echo</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>enable = nil, stderr = nil, warn = nil</span><span class='tstring_end'>&quot;</span></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'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Sequence Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. Possible cause: input file is not FASTA or the --type parameter is incorrect.\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit'>exit</span>
-  <span class='kw'>rescue</span> <span class='const'>FileNotFoundException</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$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'>. 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="fasta_file-instance_method">
-    - (<tt>Object</tt>) <strong>fasta_file</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute fasta_file</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-19
-20
-21</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 19</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_fasta_file'>fasta_file</span>
-  <span class='ivar'>@fasta_file</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="idx-instance_method">
-    - (<tt>Object</tt>) <strong>idx</strong>  <span class="extras">(readonly)</span>
-</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">
-21
-22
-23</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 21</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="outfmt-instance_method">
-    - (<tt>Object</tt>) <strong>outfmt</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute outfmt</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-23
-24
-25</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 23</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_outfmt'>outfmt</span>
-  <span class='ivar'>@outfmt</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">
-25
-26
-27</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 25</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="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">
-22
-23
-24</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 22</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="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">
-18
-19
-20</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 18</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>
-  </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="blast-instance_method">
-    - (<tt>Object</tt>) <strong>blast</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Calls blast according to the type of the sequence</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-79
-80
-81
-82
-83
-84
-85
-86
-87
-88
-89
-90
-91
-92
-93
-94
-95
-96
-97
-98
-99
-100
-101
-102
-103
-104
-105
-106
-107
-108
-109
-110
-111
-112
-113
-114
-115
-116</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 79</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_blast'>blast</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_file</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='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='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='id identifier rubyid_xml_file'>xml_file</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='ivar'>@fasta_file</span><span class='rbrace'>}</span><span class='tstring_content'>_</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_i'>i</span><span class='op'>+</span><span class='int'>1</span><span class='rbrace'>}</span><span class='tstring_content'>.xml</span><span class='tstring_end'>&quot;</span></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_xml_file'>xml_file</span> <span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>w</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_f'>f</span><span class='op'>|</span> <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='rparen'>)</span> <span class='kw'>end</span>
-          <span class='comment'>#parse output
-</span>          <span class='id identifier rubyid_parse_xml_output'>parse_xml_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='id identifier rubyid_parse_xml_output'>parse_xml_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='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'>. 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'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="call_blast_from_file-instance_method">
-    - (<tt>Object</tt>) <strong>call_blast_from_file</strong>(command, filename, gapopen, gapextend)
-</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 Output: String with
-the blast xml output</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-164
-165
-166
-167
-168
-169
-170
-171
-172
-173
-174
-175
-176
-177
-178
-179
-180
-181
-182
-183
-184
-185
-186
-187
-188
-189
-190
-191
-192</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 164</span>
-<span class='kw'>def</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='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 nr -remote -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='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'>. 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'>. Did you add BLAST path to CLASSPATH?\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-instance_method">
-    - (<tt>Object</tt>) <strong>call_blast_from_stdin</strong>(command, query, gapopen, gapextend)
-</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 Output: String with the blast xml output</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-127
-128
-129
-130
-131
-132
-133
-134
-135
-136
-137
-138
-139
-140
-141
-142
-143
-144
-145
-146
-147
-148
-149
-150
-151
-152</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 127</span>
-<span class='kw'>def</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='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 nr -remote -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='comment'>#puts &quot;Executing \&quot;#{blast_cmd}\&quot;... This may take a while...&quot;
-</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'>. 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'>. Possible cause: Did you add BLAST path to CLASSPATH?\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-instance_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">
-386
-387
-388
-389
-390
-391
-392</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 386</span>
-<span class='kw'>def</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="get_sequence_by_accession_no-instance_method">
-    - (<tt>Object</tt>) <strong>get_sequence_by_accession_no</strong>(accno, db)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Gets gene by accession number from a givem database Params: <tt>accno</tt>:
-accession number as String <tt>db</tt>: database as String Output: String
-with the nucleotide sequence corresponding to the accno</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-358
-359
-360
-361
-362
-363
-364
-365
-366
-367
-368
-369
-370
-371
-372
-373
-374
-375
-376
-377
-378</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 358</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_get_sequence_by_accession_no'>get_sequence_by_accession_no</span><span class='lparen'>(</span><span class='id identifier rubyid_accno'>accno</span><span class='comma'>,</span><span class='id identifier rubyid_db'>db</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_uri'>uri</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_db'>db</span><span class='rbrace'>}</span><span class='tstring_content'>&amp;retmax=1&amp;usehistory=y&amp;term=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_accno'>accno</span><span class='rbrace'>}</span><span class='tstring_content'>/</span><span class='tstring_end'>&quot;</span></span>
-  <span class='comment'>#puts uri
-</span>  <span class='id identifier rubyid_result'>result</span> <span class='op'>=</span> <span class='const'>Net</span><span class='op'>::</span><span class='const'>HTTP</span><span class='period'>.</span><span class='id identifier rubyid_get'>get</span><span class='lparen'>(</span><span class='const'>URI</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='id identifier rubyid_uri'>uri</span><span class='rparen'>)</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_result2'>result2</span> <span class='op'>=</span> <span class='id identifier rubyid_result'>result</span>
-  <span class='id identifier rubyid_queryKey'>queryKey</span> <span class='op'>=</span> <span class='id identifier rubyid_result2'>result2</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'>&lt;\bQueryKey\b&gt;([\w\W\d]+)&lt;\/\bQueryKey\b&gt;</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='id identifier rubyid_webEnv'>webEnv</span> <span class='op'>=</span> <span class='id identifier rubyid_result'>result</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'>&lt;\bWebEnv\b&gt;([\w\W\d]+)&lt;\/\bWebEnv\b&gt;</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='id identifier rubyid_uri'>uri</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;retmode=text&amp;retstart=0&amp;retmax=1&amp;db=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_db'>db</span><span class='rbrace'>}</span><span class='tstring_content'>&amp;query_key=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_queryKey'>queryKey</span><span class='rbrace'>}</span><span class='tstring_content'>&amp;WebEnv=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_webEnv'>webEnv</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-  <span class='id identifier rubyid_result'>result</span> <span class='op'>=</span> <span class='const'>Net</span><span class='op'>::</span><span class='const'>HTTP</span><span class='period'>.</span><span class='id identifier rubyid_get'>get</span><span class='lparen'>(</span><span class='const'>URI</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='id identifier rubyid_uri'>uri</span><span class='rparen'>)</span><span class='rparen'>)</span>
-  <span class='comment'>#parse FASTA output
-</span>  <span class='id identifier rubyid_rec'>rec</span><span class='op'>=</span><span class='id identifier rubyid_result'>result</span>
-  <span class='id identifier rubyid_nl'>nl</span> <span class='op'>=</span> <span class='id identifier rubyid_rec'>rec</span><span class='period'>.</span><span class='id identifier rubyid_index'>index</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='rparen'>)</span>
-  <span class='id identifier rubyid_header'>header</span> <span class='op'>=</span> <span class='id identifier rubyid_rec'>rec</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='id identifier rubyid_nl'>nl</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span>
-  <span class='id identifier rubyid_seq'>seq</span> <span class='op'>=</span> <span class='id identifier rubyid_rec'>rec</span><span class='lbracket'>[</span><span class='id identifier rubyid_nl'>nl</span><span class='op'>+</span><span class='int'>1</span><span class='op'>..</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span>
-  <span class='id identifier rubyid_seq'>seq</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'>\n</span><span class='regexp_end'>/</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='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="guess_sequence_type-instance_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">
-403
-404
-405
-406
-407
-408
-409
-410
-411
-412
-413
-414
-415
-416
-417
-418
-419
-420</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 403</span>
-<span class='kw'>def</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='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-instance_method">
-    - (<tt>Object</tt>) <strong>parse_next_query</strong>(iterator)
-</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 Outputs: output1: an array
-of <tt>Sequence</tt> ojbects for hits output2: <tt>Sequence</tt> object for
-the predicted sequence</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-257
-258
-259
-260
-261
-262
-263
-264
-265
-266
-267
-268
-269
-270
-271
-272
-273
-274
-275
-276
-277
-278
-279
-280
-281
-282
-283
-284
-285
-286
-287
-288
-289
-290
-291
-292
-293
-294
-295
-296
-297
-298
-299
-300
-301
-302
-303
-304
-305
-306
-307
-308
-309
-310
-311
-312
-313
-314
-315
-316
-317
-318
-319
-320
-321
-322
-323
-324
-325
-326
-327
-328
-329
-330
-331
-332
-333
-334
-335
-336
-337
-338
-339
-340
-341
-342
-343
-344
-345
-346
-347
-348
-349</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 257</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_parse_next_query'>parse_next_query</span><span class='lparen'>(</span><span class='id identifier rubyid_iterator'>iterator</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'>#puts &quot;#################################################&quot;
-</span>    <span class='comment'>#puts &quot;Parsing query #{iter.field('Iteration_iter-num')}&quot;
-</span>
-    <span class='comment'># get info about the query
-</span>    <span class='id identifier rubyid_predicted_seq'>predicted_seq</span><span class='period'>.</span><span class='id identifier rubyid_xml_length'>xml_length</span> <span class='op'>=</span> <span class='id identifier rubyid_iter'>iter</span><span class='period'>.</span><span class='id identifier rubyid_field'>field</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Iteration_query-len</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</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_predicted_seq'>predicted_seq</span><span class='period'>.</span><span class='id identifier rubyid_xml_length'>xml_length</span> <span class='op'>/=</span> <span class='int'>3</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_predicted_seq'>predicted_seq</span><span class='period'>.</span><span class='id identifier rubyid_definition'>definition</span> <span class='op'>=</span> <span class='id identifier rubyid_iter'>iter</span><span class='period'>.</span><span class='id identifier rubyid_field'>field</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Iteration_query-def</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-    <span class='comment'># parse blast the xml output and get the hits
-</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_xml_length'>xml_length</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_seq_type'>seq_type</span> <span class='op'>=</span> <span class='ivar'>@type</span>
-      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_database'>database</span> <span class='op'>=</span> <span class='id identifier rubyid_iter'>iter</span><span class='period'>.</span><span class='id identifier rubyid_field'>field</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>BlastOutput_db</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_id'>id</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='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='id identifier rubyid_species_regex'>species_regex</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='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'>if</span> <span class='id identifier rubyid_species_regex'>species_regex</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='op'>==</span> <span class='kw'>nil</span>
-        <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_species'>species</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Unknown</span><span class='tstring_end'>&quot;</span></span>
-      <span class='kw'>else</span>
-        <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_species'>species</span> <span class='op'>=</span> <span class='id identifier rubyid_species_regex'>species_regex</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='kw'>end</span>
-      <span class='comment'>#get gene by accession number
-</span>      <span class='kw'>if</span> <span class='ivar'>@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_raw_sequence'>raw_sequence</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='comment'>#get_sequence_by_accession_no(seq.accession_no, &quot;protein&quot;)
-</span>      <span class='kw'>else</span>
-        <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='comment'>#get_sequence_by_accession_no(seq.accession_no, &quot;nucleotide&quot;)
-</span>      <span class='kw'>end</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_bit_score'>bit_score</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_bit_score'>bit_score</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_hsp_score'>hsp_score</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_score'>score</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_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='ivar'>@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='int'>3</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='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='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='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_middles'>middles</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_midline'>midline</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</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_positive'>positive</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_positive'>positive</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_gaps'>gaps</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_gaps'>gaps</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_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_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='comment'>#regex = current_hsp.hseq.gsub(/[+ -]/, '+' =&gt; '.', ' ' =&gt; '.', '-' =&gt; '')
-</span>        <span class='comment'>#seq.alignment_start_offset = seq.raw_sequence.index(/#{regex}/)
-</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='comment'>#puts &quot;getting sequence #{seq.accession_no}...&quot;
-</span>    <span class='kw'>end</span>
-    <span class='kw'>return</span> <span class='lbracket'>[</span><span class='id identifier rubyid_hits'>hits</span><span class='comma'>,</span> <span class='id identifier rubyid_predicted_seq'>predicted_seq</span><span class='rbracket'>]</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'>. 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'>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="parse_xml_output-instance_method">
-    - (<tt>Object</tt>) <strong>parse_xml_output</strong>(output)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Parses the xml blast output  Param: <tt>output</tt>: <tt>String</tt> with
-the blast output in xml format</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-198
-199
-200
-201
-202
-203
-204
-205
-206
-207
-208
-209
-210
-211
-212
-213
-214
-215
-216
-217
-218
-219
-220
-221
-222
-223
-224
-225
-226
-227
-228
-229
-230
-231
-232
-233
-234
-235
-236
-237
-238
-239
-240
-241
-242
-243
-244
-245
-246
-247
-248</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 198</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_parse_xml_output'>parse_xml_output</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_iterator'>iterator</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='kw'>begin</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'>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'>iterator</span><span class='period'>.</span><span class='id identifier rubyid_next'>next</span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_sequences'>sequences</span> <span class='op'>=</span> <span class='id identifier rubyid_parse_next_query'>parse_next_query</span><span class='lparen'>(</span><span class='id identifier rubyid_iterator'>iterator</span><span class='rparen'>)</span> <span class='comment'>#returns [hits, predicted_seq]
-</span>      <span class='kw'>if</span> <span class='id identifier rubyid_sequences'>sequences</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_hits'>hits</span> <span class='op'>=</span> <span class='id identifier rubyid_sequences'>sequences</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
-      <span class='id identifier rubyid_prediction'>prediction</span> <span class='op'>=</span> <span class='id identifier rubyid_sequences'>sequences</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
-      <span class='comment'># get the @idx-th sequence  from the fasta file
-</span>      <span class='id identifier rubyid_i'>i</span> <span class='op'>=</span> <span class='ivar'>@idx</span><span class='op'>-</span><span class='int'>1</span>
-      <span class='comment'>### add exception
-</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_file</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='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_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'>[^\n]*\n([ATGCatgc\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='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='comment'>#file seek for each query
-</span>
-      <span class='comment'># do validations
-</span>
-      <span class='id identifier rubyid_v'>v</span> <span class='op'>=</span> <span class='const'>Validation</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_hits'>hits</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='ivar'>@type</span><span class='comma'>,</span> <span class='ivar'>@fasta_file</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='kw'>if</span> <span class='ivar'>@outfmt</span> <span class='op'>==</span> <span class='symbol'>:html</span>
-        <span class='id identifier rubyid_query_output'>query_output</span> <span class='op'>=</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validate_all'>validate_all</span><span class='lparen'>(</span><span class='kw'>true</span><span class='rparen'>)</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='kw'>else</span>
-        <span class='id identifier rubyid_query_output'>query_output</span> <span class='op'>=</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validate_all'>validate_all</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_print_output_console'>print_output_console</span>
-      <span class='comment'>#if @outfmt == :yaml
-</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='comment'>#end
-</span>    <span class='kw'>end</span>
-    <span class='kw'>rescue</span> <span class='const'>NoMethodError</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'>NoMethod 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'>. Possible cause: input file is not in blast xml format.\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'>return</span>
-  <span class='kw'>end</span> <span class='kw'>while</span> <span class='int'>1</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="type_of_sequences-instance_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">
-432
-433
-434
-435
-436
-437
-438
-439
-440
-441
-442
-443
-444
-445
-446</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 432</span>
-<span class='kw'>def</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='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'>ArgumentError</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Insufficient info to determine sequence type. Cleaned queries are: </span><span class='embexpr_beg'>#{</span> <span class='id identifier rubyid_sequences'>sequences</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span> <span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Wed Aug  7 01:58:44 2013 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7 (ruby-1.9.3).
-</div>
-  </body>
-</html>