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

genevalidator 1.6.1 → 1.6.2

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

Files changed (131) hide show

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

data/doc/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>