bio-gngm 0.1.0

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  2. data/Gemfile +20 -0
  3. data/Gemfile.lock +33 -0
  4. data/LICENSE.txt +20 -0
  5. data/README.rdoc +33 -0
  6. data/Rakefile +53 -0
  7. data/VERSION +1 -0
  8. data/bio-gngm.gemspec +173 -0
  9. data/doc/Bio.html +129 -0
  10. data/doc/Bio/DB.html +128 -0
  11. data/doc/Bio/DB/Pileup.html +316 -0
  12. data/doc/Bio/DB/Vcf.html +683 -0
  13. data/doc/Bio/Util.html +135 -0
  14. data/doc/Bio/Util/Gngm.html +1655 -0
  15. data/doc/LICENSE_txt.html +111 -0
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  59. data/doc/js/search_index.js +1 -0
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  61. data/doc/lib/bio-gngm_rb.html +103 -0
  62. data/doc/lib/bio/util/bio-gngm_rb.html +96 -0
  63. data/doc/method_list.html +382 -0
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  66. data/examples/.DS_Store +0 -0
  67. data/examples/make_histograms.rb +40 -0
  68. data/examples/make_threads.rb +42 -0
  69. data/examples/make_threads_isize.rb +41 -0
  70. data/examples/use_indels.rb +36 -0
  71. data/lib/bio-gngm.rb +12 -0
  72. data/lib/bio/util/bio-gngm.rb +1029 -0
  73. data/scripts/get_subseq.rb +16 -0
  74. data/scripts/make_histograms_laerfyve.rb +83 -0
  75. data/scripts/make_histograms_laerfyve_stitched.rb +59 -0
  76. data/scripts/make_threads_isize_laerfyfe.rb +52 -0
  77. data/scripts/make_threads_unmapped_laerfyfe.rb +72 -0
  78. data/scripts/make_threads_unmapped_laerfyfe_pseudo.rb +56 -0
  79. data/scripts/make_threads_unmapped_simulation.rb +54 -0
  80. data/scripts/make_threads_unmapped_simulation_immediate_region.rb +59 -0
  81. data/scripts/optimise_freq_window_size.rb +82 -0
  82. data/stitched_contigs.zip +0 -0
  83. data/test/data/ids2.txt +1 -0
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  101. data/test/data/testu.bam +0 -0
  102. data/test/data/testu.bam.bai +0 -0
  103. data/test/helper.rb +18 -0
  104. data/test/test_bio-gngm.rb +126 -0
  105. metadata +276 -0
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+ <li>lib/bio/util/bio-gngm.rb
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+ </nav>
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+ <!-- Method Quickref -->
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+ <h3 class="section-header">Methods</h3>
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+ <ul class="link-list">
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+ <li><a href="#method-i-discordant_chastity">#discordant_chastity</a>
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+ <li><a href="../../Bio/Util.html">Bio::Util</a>
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+ <div id="documentation">
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+ <h1 class="class">class Bio::DB::Pileup</h1>
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+
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+ <div id="description" class="description">
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+
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+ <p>Extends the methods of the <a href="Pileup.html">Bio::DB::Pileup</a> class
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+ in bio-samtools. A pileup object represents the SAMtools pileup format at
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+ <a
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+ href="http://samtools.sourceforge.net/pileup.shtml.">samtools.sourceforge.net/pileup.shtml.</a>
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+ These extension methods are used by the <a
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+ href="../Util/Gngm.html">Bio::Util::Gngm</a> object internally and are not
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+ exposed to the user of the <a href="../Util/Gngm.html">Bio::Util::Gngm</a>
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+ object through that.</p>
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+
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+ </div><!-- description -->
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+
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+ <section id="5Buntitled-5D" class="documentation-section">
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+
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+
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+
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+ <!-- Attributes -->
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+ <section id="attribute-method-details" class="method-section section">
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+ <h3 class="section-header">Attributes</h3>
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+
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+
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+ <div id="attribute-i-second_non_ref_count" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">second_non_ref_count</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+ <p>attributes set by call to <a
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+ href="Pileup.html#method-i-discordant_chastity">#discordant_chastity</a></p>
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-third_non_ref_count" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">third_non_ref_count</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+ <p>attributes set by call to <a
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+ href="Pileup.html#method-i-discordant_chastity">#discordant_chastity</a></p>
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-top_non_ref_count" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">top_non_ref_count</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+ <p>attributes set by call to <a
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+ href="Pileup.html#method-i-discordant_chastity">#discordant_chastity</a></p>
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+
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+ </div>
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+ </div>
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+
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+ </section><!-- attribute-method-details -->
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+
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+
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+ <!-- Methods -->
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+
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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Instance Methods</h3>
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+
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+
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+ <div id="method-i-discordant_chastity" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">discordant_chastity</span><span
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+ class="method-args">()</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
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+
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+ <div class="method-description">
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+
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+ <p>calculates the discordant chastity statistic as defined in Austin et al
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+ (2011) <a
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+ href="http://bar.utoronto.ca/ngm/description.html">bar.utoronto.ca/ngm/description.html</a>
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+ and <a
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+ href="http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04619.x/abstract;jsessionid=F73E2DA628523B26205297CEE95526DA.d02t04">onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04619.x/abstract;jsessionid=F73E2DA628523B26205297CEE95526DA.d02t04</a>
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+ Austin <em>et</em> <em>al</em> (2011) <strong>Next-generation</strong>
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+ <strong>mapping</strong> <strong>of</strong> <strong>Arabidopsis</strong>
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+ <strong>genes</strong> <em>Plant</em> <em>Journal</em>
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+ <strong>67</strong>(4):7125-725</p>
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+
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+ <p>Briefly,</p>
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+
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+ <pre>The statistic measures the degree of difference between the SNP and the expected reference base.
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+ Using the mapping information comprising a SNP, the most frequent base that is not the reference base
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+ is compared to the next most common base after it.
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+ (from http://bar.utoronto.ca/ngm/description.html )</pre>
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+
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+
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+
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+ <div class="method-source-code" id="discordant_chastity-source">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 33</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">discordant_chastity</span>
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+ <span class="ruby-identifier">arr</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_refs</span>.<span class="ruby-identifier">to_a</span>.<span class="ruby-identifier">sort</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">a</span>,<span class="ruby-identifier">b</span><span class="ruby-operator">|</span> <span class="ruby-identifier">b</span>.<span class="ruby-identifier">last</span> <span class="ruby-operator">&lt;=&gt;</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">last</span> }
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+ <span class="ruby-ivar">@top_non_ref_count</span>, <span class="ruby-ivar">@second_non_ref_count</span>, <span class="ruby-ivar">@third_non_ref_count</span> = <span class="ruby-identifier">arr</span>.<span class="ruby-identifier">collect</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">c</span><span class="ruby-operator">|</span> <span class="ruby-identifier">c</span>.<span class="ruby-identifier">last</span>}
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+ <span class="ruby-keyword">case</span>
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+ <span class="ruby-keyword">when</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_ref_count</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span> <span class="ruby-keyword">then</span> <span class="ruby-value">0.0</span>
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+ <span class="ruby-keyword">when</span> <span class="ruby-ivar">@top_non_ref_count</span> <span class="ruby-operator">==</span> <span class="ruby-ivar">@coverage</span> <span class="ruby-keyword">then</span> <span class="ruby-value">1.0</span>
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+ <span class="ruby-keyword">when</span> <span class="ruby-ivar">@second_non_ref_count</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span> <span class="ruby-keyword">then</span> <span class="ruby-ivar">@top_non_ref_count</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> (<span class="ruby-ivar">@top_non_ref_count</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@second_non_ref_count</span>).<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-keyword">else</span> <span class="ruby-ivar">@top_non_ref_count</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- discordant_chastity-source -->
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+
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+ </div>
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+
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+
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+
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+
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+ </div><!-- discordant_chastity-method -->
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+
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+
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+ <div id="method-i-is_snp-3F" class="method-detail ">
252
+
253
+ <div class="method-heading">
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+ <span class="method-name">is_snp?</span><span
255
+ class="method-args">(opts)</span>
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+ <span class="method-click-advice">click to toggle source</span>
257
+ </div>
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+
259
+
260
+ <div class="method-description">
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+
262
+ <p>returns true if self is a SNP with minimum coverage depth of
263
+ <code>:min_depth</code> and minimum non-reference bases of
264
+ <code>:min_non_ref_count</code> returns false for every position where the
265
+ reference base is N or n if <code>:ignore_reference_n</code> is set to true</p>
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+
267
+ <p>Options and Defaults:</p>
268
+ <ul><li>
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+ <p>:min_depth =&gt; 2</p>
270
+ </li><li>
271
+ <p>:min_non_ref_count =&gt; 2</p>
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+ </li><li>
273
+ <p>:ignore_reference_n =&gt; false</p>
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+ </li></ul>
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+
276
+ <p>Example</p>
277
+
278
+ <pre class="ruby"><span class="ruby-identifier">pileup</span>.<span class="ruby-identifier">is_snp?</span>(:<span class="ruby-identifier">min_depth</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">5</span>, :<span class="ruby-identifier">min_non_ref_count</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">2</span>)
279
+ <span class="ruby-identifier">pileup</span>.<span class="ruby-identifier">is_snp?</span>(:<span class="ruby-identifier">min_depth</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">5</span>, :<span class="ruby-identifier">min_non_ref_count</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>, :<span class="ruby-identifier">ignore_reference_n</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">true</span>)
280
+ </pre>
281
+
282
+
283
+
284
+ <div class="method-source-code" id="is_snp-3F-source">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 55</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_snp?</span>(<span class="ruby-identifier">opts</span>)
287
+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:ignore_reference_n</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">&quot;N&quot;</span> <span class="ruby-keyword">or</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">&quot;n&quot;</span>
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+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span>
289
+ <span class="ruby-keyword">elsif</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">coverage</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:min_depth</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_ref_count</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:min_non_ref_count</span>]
290
+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span>
291
+ <span class="ruby-keyword">end</span>
292
+ <span class="ruby-keyword">false</span>
293
+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- is_snp-3F-source -->
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+
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+ </div>
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+
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+
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+
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+
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+ </div><!-- is_snp-3F-method -->
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+
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+
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+ </section><!-- public-instance-method-details -->
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+
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+ </section><!-- 5Buntitled-5D -->
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+
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+ </div><!-- documentation -->
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+
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+
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+ <footer id="validator-badges">
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+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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+ </footer>
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+
data/doc/Bio/DB/Vcf.html ADDED
@@ -0,0 +1,683 @@
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+ <!DOCTYPE html>
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+
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+ <html>
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+
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+ <title>Class: Bio::DB::Vcf</title>
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+
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+ <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
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+
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "../../";
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+ <script type="text/javascript" charset="utf-8" src="../../js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/darkfish.js"></script>
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+
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+ <body id="top" class="class">
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+ <nav id="metadata">
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+ <nav id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../../index.html">Home</a>
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+ <a href="../../table_of_contents.html#classes">Classes</a>
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+ <a href="../../table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ </nav>
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+
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+
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </h3>
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+ </form>
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+
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+ <ul id="search-results" class="initially-hidden"></ul>
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+ </nav>
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+
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+
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+ <div id="file-metadata">
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+ <nav id="file-list-section" class="section">
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+ <h3 class="section-header">Defined In</h3>
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+ <ul>
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+ <li>lib/bio/util/bio-gngm.rb
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+ </ul>
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+ </nav>
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+
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+
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+ </div>
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+
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+ <div id="class-metadata">
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+
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+ <nav id="parent-class-section" class="section">
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+ <h3 class="section-header">Parent</h3>
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+
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+ <p class="link">Object
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+
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+ </nav>
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+
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+
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+ <!-- Method Quickref -->
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+ <nav id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="#method-i-alternatives">#alternatives</a>
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+
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+ <li><a href="#method-i-gq">#gq</a>
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+
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+ <li><a href="#method-i-has_just_one_variant-3F">#has_just_one_variant?</a>
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+
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+ <li><a href="#method-i-is_deletion-3F">#is_deletion?</a>
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+
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+ <li><a href="#method-i-is_indel-3F">#is_indel?</a>
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+
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+ <li><a href="#method-i-is_insertion-3F">#is_insertion?</a>
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+
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+ <li><a href="#method-i-mq">#mq</a>
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+
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+ <li><a href="#method-i-non_ref_allele_count">#non_ref_allele_count</a>
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+
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+ <li><a href="#method-i-non_ref_allele_freq">#non_ref_allele_freq</a>
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+
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+ <li><a href="#method-i-pass_quality-3F">#pass_quality?</a>
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+
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+ <li><a href="#method-i-pl">#pl</a>
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+
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+ <li><a href="#method-i-to_s">#to_s</a>
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+
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+ <li><a href="#method-i-used_depth">#used_depth</a>
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+
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+ <li><a href="#method-i-variant-3F">#variant?</a>
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+
101
+ </ul>
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+ </nav>
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+
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+ </div>
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+
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+ <div id="project-metadata">
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+ <nav id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Pages</h3>
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+
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+ <ul>
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+
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+ <li class="file"><a href="../../LICENSE_txt.html">LICENSE</a>
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+
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+ </ul>
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+ </nav>
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+
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="../../Bio.html">Bio</a>
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+
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+ <li><a href="../../Bio/DB.html">Bio::DB</a>
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+
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+ <li><a href="../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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+
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+ <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
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+
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+ <li><a href="../../Bio/Util.html">Bio::Util</a>
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+
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+ <li><a href="../../Bio/Util/Gngm.html">Bio::Util::Gngm</a>
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+
134
+ </ul>
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+ </nav>
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+
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+ </div>
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+ </nav>
139
+
140
+ <div id="documentation">
141
+ <h1 class="class">class Bio::DB::Vcf</h1>
142
+
143
+ <div id="description" class="description">
144
+
145
+ <p>Extends the methods of the <a href="Vcf.html">Bio::DB::Vcf</a> class in
146
+ bio-samtools. A <a href="Vcf.html">Vcf</a> object represents the VCF format
147
+ described at <a
148
+ href="http://www.1000genomes.org/node/101">www.1000genomes.org/node/101</a>
149
+ . The <a href="Vcf.html">Bio::DB::Vcf</a> object returns all information in
150
+ the VCF line, but the implementation here acts as if there is only possibly
151
+ one variant at each position and ignores positions at which there may be
152
+ multiple variants. <a href="Vcf.html">Vcf</a> format is only used when the
153
+ <a href="../Util/Gngm.html">Bio::Util::Gngm</a> object requests information
154
+ about indels using SAMtools mpileup method.</p>
155
+
156
+ </div><!-- description -->
157
+
158
+
159
+
160
+
161
+ <section id="5Buntitled-5D" class="documentation-section">
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+
163
+
164
+
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+
166
+
167
+
168
+
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+
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+ <!-- Methods -->
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+
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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Instance Methods</h3>
174
+
175
+
176
+ <div id="method-i-alternatives" class="method-detail ">
177
+
178
+ <div class="method-heading">
179
+ <span class="method-name">alternatives</span><span
180
+ class="method-args">()</span>
181
+ <span class="method-click-advice">click to toggle source</span>
182
+ </div>
183
+
184
+
185
+ <div class="method-description">
186
+
187
+ <p>List of alternate alleles at this locus, obtained by splitting the vcf.alt
188
+ attribute string on commas</p>
189
+
190
+ <p>Example vcf.alt = “ACT,TCA”</p>
191
+
192
+ <pre>vcf.alternatives = [&quot;ACT&quot;, &quot;TCA&quot;]</pre>
193
+
194
+ <p>vcf.alt = “T”</p>
195
+
196
+ <pre>vcf.alternatives = [&quot;T&quot;]</pre>
197
+
198
+
199
+
200
+ <div class="method-source-code" id="alternatives-source">
201
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 101</span>
202
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">alternatives</span>
203
+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alt</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;,&quot;</span>) <span class="ruby-keyword">rescue</span> []
204
+ <span class="ruby-keyword">end</span></pre>
205
+ </div><!-- alternatives-source -->
206
+
207
+ </div>
208
+
209
+
210
+
211
+
212
+ </div><!-- alternatives-method -->
213
+
214
+
215
+ <div id="method-i-gq" class="method-detail ">
216
+
217
+ <div class="method-heading">
218
+ <span class="method-name">gq</span><span
219
+ class="method-args">()</span>
220
+ <span class="method-click-advice">click to toggle source</span>
221
+ </div>
222
+
223
+
224
+ <div class="method-description">
225
+
226
+ <p>Returns the genotype quality score from the sample data (as defined by the
227
+ <a href="Vcf.html">Vcf</a> GQ attribute) for the first sample in the <a
228
+ href="Vcf.html">Vcf</a> only.</p>
229
+
230
+
231
+
232
+ <div class="method-source-code" id="gq-source">
233
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 124</span>
234
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">gq</span>
235
+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">samples</span>[<span class="ruby-string">&quot;1&quot;</span>][<span class="ruby-string">&quot;GQ&quot;</span>].<span class="ruby-identifier">to_f</span> <span class="ruby-keyword">rescue</span> <span class="ruby-value">0.0</span>
236
+ <span class="ruby-keyword">end</span></pre>
237
+ </div><!-- gq-source -->
238
+
239
+ </div>
240
+
241
+
242
+
243
+
244
+ </div><!-- gq-method -->
245
+
246
+
247
+ <div id="method-i-has_just_one_variant-3F" class="method-detail ">
248
+
249
+ <div class="method-heading">
250
+ <span class="method-name">has_just_one_variant?</span><span
251
+ class="method-args">()</span>
252
+ <span class="method-click-advice">click to toggle source</span>
253
+ </div>
254
+
255
+
256
+ <div class="method-description">
257
+
258
+ <p>Returns true if only one variant allele is recorded. Loci with more than
259
+ one allele are too complicated for now, so are discarded…</p>
260
+
261
+
262
+
263
+ <div class="method-source-code" id="has_just_one_variant-3F-source">
264
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 134</span>
265
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">has_just_one_variant?</span>
266
+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alternatives</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span> <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">variant?</span>
267
+ <span class="ruby-keyword">end</span></pre>
268
+ </div><!-- has_just_one_variant-3F-source -->
269
+
270
+ </div>
271
+
272
+
273
+
274
+
275
+ </div><!-- has_just_one_variant-3F-method -->
276
+
277
+
278
+ <div id="method-i-is_deletion-3F" class="method-detail ">
279
+
280
+ <div class="method-heading">
281
+ <span class="method-name">is_deletion?</span><span
282
+ class="method-args">(options)</span>
283
+ <span class="method-click-advice">click to toggle source</span>
284
+ </div>
285
+
286
+
287
+ <div class="method-description">
288
+
289
+ <p>Returns true if the length of the alt column is less than that of the ref
290
+ column in the <a href="Vcf.html">Vcf</a> and if <a
291
+ href="Vcf.html#method-i-pass_quality-3F">#pass_quality?</a> is true. Looks
292
+ only at the positions that are predicted simple deletions, any positions
293
+ where the alt alleles includes more than one deletion or a SNP or an
294
+ insertion also is ignored.</p>
295
+
296
+
297
+
298
+ <div class="method-source-code" id="is_deletion-3F-source">
299
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 153</span>
300
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_deletion?</span>(<span class="ruby-identifier">options</span>)
301
+ <span class="ruby-keyword">case</span>
302
+ <span class="ruby-keyword">when</span> (<span class="ruby-keyword">not</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">has_just_one_variant?</span>) <span class="ruby-keyword">then</span> <span class="ruby-keyword">false</span>
303
+ <span class="ruby-keyword">when</span> ( <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alt</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">&lt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref</span>.<span class="ruby-identifier">length</span> <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pass_quality?</span>(<span class="ruby-identifier">options</span>) ) <span class="ruby-keyword">then</span> <span class="ruby-keyword">true</span>
304
+ <span class="ruby-keyword">else</span> <span class="ruby-keyword">false</span>
305
+ <span class="ruby-keyword">end</span>
306
+ <span class="ruby-keyword">rescue</span> <span class="ruby-comment">## if something goes wrong, skip the postion, </span>
307
+ <span class="ruby-keyword">false</span>
308
+ <span class="ruby-keyword">end</span></pre>
309
+ </div><!-- is_deletion-3F-source -->
310
+
311
+ </div>
312
+
313
+
314
+
315
+
316
+ </div><!-- is_deletion-3F-method -->
317
+
318
+
319
+ <div id="method-i-is_indel-3F" class="method-detail ">
320
+
321
+ <div class="method-heading">
322
+ <span class="method-name">is_indel?</span><span
323
+ class="method-args">(opts)</span>
324
+ <span class="method-click-advice">click to toggle source</span>
325
+ </div>
326
+
327
+
328
+ <div class="method-description">
329
+
330
+ <p>Returns true if either <a
331
+ href="Vcf.html#method-i-is_insertion-3F">#is_insertion?</a> or <a
332
+ href="Vcf.html#method-i-is_deletion-3F">#is_deletion?</a> is true</p>
333
+
334
+
335
+
336
+ <div class="method-source-code" id="is_indel-3F-source">
337
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 176</span>
338
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_indel?</span>(<span class="ruby-identifier">opts</span>)
339
+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">is_insertion?</span>(<span class="ruby-identifier">opts</span>) <span class="ruby-operator">||</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">is_deletion?</span>(<span class="ruby-identifier">opts</span>)
340
+ <span class="ruby-keyword">end</span></pre>
341
+ </div><!-- is_indel-3F-source -->
342
+
343
+ </div>
344
+
345
+
346
+
347
+
348
+ </div><!-- is_indel-3F-method -->
349
+
350
+
351
+ <div id="method-i-is_insertion-3F" class="method-detail ">
352
+
353
+ <div class="method-heading">
354
+ <span class="method-name">is_insertion?</span><span
355
+ class="method-args">(options)</span>
356
+ <span class="method-click-advice">click to toggle source</span>
357
+ </div>
358
+
359
+
360
+ <div class="method-description">
361
+
362
+ <p>Returns true if the length of the alt column is greater than that of the
363
+ ref column in the <a href="Vcf.html">Vcf</a> and if <a
364
+ href="Vcf.html#method-i-pass_quality-3F">#pass_quality?</a> is true. Looks
365
+ only at the positions that are predicted simple deletions, any positions
366
+ where the alt alleles includes more than one deletion or a SNP or an
367
+ insertion also is ignored.</p>
368
+
369
+
370
+
371
+ <div class="method-source-code" id="is_insertion-3F-source">
372
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 165</span>
373
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_insertion?</span>(<span class="ruby-identifier">options</span>)
374
+ <span class="ruby-keyword">case</span>
375
+ <span class="ruby-keyword">when</span> (<span class="ruby-keyword">not</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">has_just_one_variant?</span>) <span class="ruby-keyword">then</span> <span class="ruby-keyword">false</span>
376
+ <span class="ruby-keyword">when</span> ( <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alt</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref</span>.<span class="ruby-identifier">length</span> <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pass_quality?</span>(<span class="ruby-identifier">options</span>) ) <span class="ruby-keyword">then</span> <span class="ruby-keyword">true</span>
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+ <span class="ruby-keyword">else</span> <span class="ruby-keyword">false</span>
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-keyword">rescue</span> <span class="ruby-comment">## if something goes wrong, skip the postion, </span>
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+ <span class="ruby-keyword">false</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- is_insertion-3F-source -->
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+
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+ </div>
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+
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+
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+
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+
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+ </div><!-- is_insertion-3F-method -->
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+
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+
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+ <div id="method-i-mq" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">mq</span><span
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+ class="method-args">()</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
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+
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+ <div class="method-description">
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+
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+ <p>Returns the mean Mapping Quality from the reads over this position as
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+ defined by the <a href="Vcf.html">Vcf</a> MQ attribute.</p>
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+
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+
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+
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+ <div class="method-source-code" id="mq-source">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 119</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">mq</span>
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+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">info</span>[<span class="ruby-string">&quot;MQ&quot;</span>].<span class="ruby-identifier">to_f</span> <span class="ruby-keyword">rescue</span> <span class="ruby-value">0.0</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- mq-source -->
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+
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+ </div>
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+
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+
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+
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+
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+ </div><!-- mq-method -->
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+
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+
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+ <div id="method-i-non_ref_allele_count" class="method-detail ">
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+
425
+ <div class="method-heading">
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+ <span class="method-name">non_ref_allele_count</span><span
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+ class="method-args">()</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
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+
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+ <div class="method-description">
433
+
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+ <p>Returns the depth of reads containing the non reference allele. IE the sum
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+ of the last two figures in the DP4 attribute.</p>
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+
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+
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+
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+ <div class="method-source-code" id="non_ref_allele_count-source">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 106</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">non_ref_allele_count</span>
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+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">info</span>[<span class="ruby-string">&quot;DP4&quot;</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;,&quot;</span>)[<span class="ruby-value">2</span><span class="ruby-operator">..</span><span class="ruby-value">3</span>].<span class="ruby-identifier">inject</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">sum</span>,<span class="ruby-identifier">n</span><span class="ruby-operator">|</span> <span class="ruby-identifier">sum</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">n</span>.<span class="ruby-identifier">to_f</span> } <span class="ruby-keyword">rescue</span> <span class="ruby-value">0.0</span>
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+ <span class="ruby-keyword">end</span></pre>
444
+ </div><!-- non_ref_allele_count-source -->
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+
446
+ </div>
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+
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+
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+
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+
451
+ </div><!-- non_ref_allele_count-method -->
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+
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+
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+ <div id="method-i-non_ref_allele_freq" class="method-detail ">
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+
456
+ <div class="method-heading">
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+ <span class="method-name">non_ref_allele_freq</span><span
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+ class="method-args">()</span>
459
+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
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+
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+ <div class="method-description">
464
+
465
+ <p>Returns the non-reference allele frequency based on depth of reads used for
466
+ the genotype call,</p>
467
+
468
+ <p>IE</p>
469
+
470
+ <pre>vcf.non_ref_allele_count / vcf.used_depth</pre>
471
+
472
+
473
+
474
+ <div class="method-source-code" id="non_ref_allele_freq-source">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 114</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">non_ref_allele_freq</span>
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+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_ref_allele_count</span> <span class="ruby-operator">/</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">used_depth</span>
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+ <span class="ruby-keyword">end</span></pre>
479
+ </div><!-- non_ref_allele_freq-source -->
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+
481
+ </div>
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+
483
+
484
+
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+
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+ </div><!-- non_ref_allele_freq-method -->
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+
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+
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+ <div id="method-i-pass_quality-3F" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">pass_quality?</span><span
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+ class="method-args">(options)</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
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+
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+ <div class="method-description">
499
+
500
+ <p>Returns true if the position passes criteria</p>
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+
502
+ <p>Options and Defaults:</p>
503
+ <ul><li>
504
+ <p>:min_depth =&gt; 2</p>
505
+ </li><li>
506
+ <p>:min_non_ref_count =&gt; 2</p>
507
+ </li><li>
508
+ <p>:mapping_quality =&gt; 10</p>
509
+ </li></ul>
510
+
511
+ <p>Example</p>
512
+
513
+ <pre class="ruby"><span class="ruby-identifier">vcf</span>.<span class="ruby-identifier">pass_quality?</span>(:<span class="ruby-identifier">min_depth</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">5</span>, :<span class="ruby-identifier">min_non_ref_count</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">2</span>, :<span class="ruby-identifier">mapping_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">25</span>)
514
+ </pre>
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+
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+
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+
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+ <div class="method-source-code" id="pass_quality-3F-source">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 147</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">pass_quality?</span>(<span class="ruby-identifier">options</span>)
521
+ (<span class="ruby-keyword">self</span>.<span class="ruby-identifier">used_depth</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:min_depth</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">mq</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:mapping_quality</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_ref_allele_count</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:min_non_ref_count</span>])
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+ <span class="ruby-keyword">end</span></pre>
523
+ </div><!-- pass_quality-3F-source -->
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+
525
+ </div>
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+
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+
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+
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+
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+ </div><!-- pass_quality-3F-method -->
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+
532
+
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+ <div id="method-i-pl" class="method-detail ">
534
+
535
+ <div class="method-heading">
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+ <span class="method-name">pl</span><span
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+ class="method-args">()</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
541
+
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+ <div class="method-description">
543
+
544
+ <p>Returns the phred scaled likelihood of the first non-reference allele (as
545
+ defined by the <a href="Vcf.html">Vcf</a> PL attribute) for the first
546
+ sample in the <a href="Vcf.html">Vcf</a> only.</p>
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+
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+
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+
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+ <div class="method-source-code" id="pl-source">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 129</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">pl</span>
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+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">samples</span>[<span class="ruby-string">&quot;1&quot;</span>][<span class="ruby-string">&quot;PL&quot;</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;,&quot;</span>)[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_f</span> <span class="ruby-keyword">rescue</span> <span class="ruby-value">0.0</span>
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+ <span class="ruby-keyword">end</span></pre>
555
+ </div><!-- pl-source -->
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+
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+ </div>
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+
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+
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+
561
+
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+ </div><!-- pl-method -->
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+
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+
565
+ <div id="method-i-to_s" class="method-detail ">
566
+
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+ <div class="method-heading">
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+ <span class="method-name">to_s</span><span
569
+ class="method-args">()</span>
570
+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
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+
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+ <div class="method-description">
575
+
576
+ <p>Return a short string representing chromosome, position, reference
577
+ sequence, alt sequence(s) and the info string of the <a
578
+ href="Vcf.html">Vcf</a> object.</p>
579
+
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+
581
+
582
+ <div class="method-source-code" id="to_s-source">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 85</span>
584
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_s</span>
585
+ <span class="ruby-node">&quot;#{self.chrom} #{self.pos} #{self.ref} #{self.alt} #{self.info}&quot;</span>
586
+ <span class="ruby-keyword">end</span></pre>
587
+ </div><!-- to_s-source -->
588
+
589
+ </div>
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+
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+
592
+
593
+
594
+ </div><!-- to_s-method -->
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+
596
+
597
+ <div id="method-i-used_depth" class="method-detail ">
598
+
599
+ <div class="method-heading">
600
+ <span class="method-name">used_depth</span><span
601
+ class="method-args">()</span>
602
+ <span class="method-click-advice">click to toggle source</span>
603
+ </div>
604
+
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+
606
+ <div class="method-description">
607
+
608
+ <p>The depth of reads actually used in the genotype call by Vcftools. The sum
609
+ of the DP4 attribute. Returns 0.0 if no value is calculated.</p>
610
+
611
+
612
+
613
+ <div class="method-source-code" id="used_depth-source">
614
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 90</span>
615
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">used_depth</span>
616
+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">info</span>[<span class="ruby-string">&quot;DP4&quot;</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;,&quot;</span>).<span class="ruby-identifier">inject</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">sum</span>,<span class="ruby-identifier">n</span><span class="ruby-operator">|</span> <span class="ruby-identifier">sum</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">n</span>.<span class="ruby-identifier">to_f</span>} <span class="ruby-keyword">rescue</span> <span class="ruby-value">0.0</span>
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+ <span class="ruby-keyword">end</span></pre>
618
+ </div><!-- used_depth-source -->
619
+
620
+ </div>
621
+
622
+
623
+
624
+
625
+ </div><!-- used_depth-method -->
626
+
627
+
628
+ <div id="method-i-variant-3F" class="method-detail ">
629
+
630
+ <div class="method-heading">
631
+ <span class="method-name">variant?</span><span
632
+ class="method-args">()</span>
633
+ <span class="method-click-advice">click to toggle source</span>
634
+ </div>
635
+
636
+
637
+ <div class="method-description">
638
+
639
+ <p>returns true if the <code>alt</code> column of the <a
640
+ href="Vcf.html">Vcf</a> is not <strong>.</strong></p>
641
+
642
+ <p>Examples</p>
643
+
644
+ <p>vcf record = 20 14370 rs6054257 G A 29 PASS …</p>
645
+
646
+ <pre class="ruby"><span class="ruby-identifier">vcf</span>.<span class="ruby-identifier">variant?</span> <span class="ruby-comment">#=&gt; true</span>
647
+ </pre>
648
+
649
+ <p>vcf record = 20 1230237 . T . 47 PASS …</p>
650
+
651
+ <pre class="ruby"><span class="ruby-identifier">vcf</span>.<span class="ruby-identifier">variant?</span> <span class="ruby-comment">#=&gt; false</span>
652
+ </pre>
653
+
654
+
655
+
656
+ <div class="method-source-code" id="variant-3F-source">
657
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 80</span>
658
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">variant?</span>
659
+ <span class="ruby-keyword">not</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alt</span> <span class="ruby-operator">==</span> <span class="ruby-string">&quot;.&quot;</span> <span class="ruby-keyword">rescue</span> <span class="ruby-keyword">false</span>
660
+ <span class="ruby-keyword">end</span></pre>
661
+ </div><!-- variant-3F-source -->
662
+
663
+ </div>
664
+
665
+
666
+
667
+
668
+ </div><!-- variant-3F-method -->
669
+
670
+
671
+ </section><!-- public-instance-method-details -->
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+
673
+ </section><!-- 5Buntitled-5D -->
674
+
675
+ </div><!-- documentation -->
676
+
677
+
678
+ <footer id="validator-badges">
679
+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
680
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
681
+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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+ </footer>
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+