bio-gngm 0.2.0 → 0.2.1

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Files changed (25) hide show
  1. data/VERSION +1 -1
  2. data/bio-gngm.gemspec +7 -3
  3. data/doc/Bio.html +4 -2
  4. data/doc/Bio/DB.html +4 -2
  5. data/doc/Bio/DB/FastaLengthDB.html +238 -0
  6. data/doc/Bio/DB/Pileup.html +10 -9
  7. data/doc/Bio/DB/Vcf.html +52 -102
  8. data/doc/Bio/Util.html +4 -2
  9. data/doc/Bio/Util/Gngm.html +318 -72
  10. data/doc/LICENSE_txt.html +12 -9
  11. data/doc/created.rid +3 -3
  12. data/doc/index.html +3 -1
  13. data/doc/js/search_index.js +1 -1
  14. data/doc/lib/bio-gngm_rb.html +2 -0
  15. data/doc/lib/bio/util/bio-gngm_rb.html +2 -0
  16. data/doc/table_of_contents.html +20 -7
  17. data/examples/Chr1.html +1483 -0
  18. data/examples/gngm_qtl_mapping_HTML_maker_set_options.rb +243 -0
  19. data/examples/pileup.txt +22 -0
  20. data/examples/snps.vcf +22 -0
  21. data/lib/bio-gngm.rb +0 -1
  22. data/lib/bio/util/bio-gngm.rb +100 -38
  23. data/test/test_bio-gngm.rb +1 -1
  24. metadata +30 -26
  25. data/lib/bio/util/mutation_effects.rb +0 -39
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.2.0
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+ 0.2.1
data/bio-gngm.gemspec CHANGED
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = "bio-gngm"
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- s.version = "0.2.0"
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+ s.version = "0.2.1"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Dan MacLean"]
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- s.date = "2012-11-15"
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+ s.date = "2012-12-06"
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  s.description = "Identify causative mutations in a model genome from NGS reads using the NGM method."
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  s.email = "maclean.daniel@gmail.com"
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  s.extra_rdoc_files = [
@@ -27,6 +27,7 @@ Gem::Specification.new do |s|
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  "bio-gngm.gemspec",
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  "doc/Bio.html",
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  "doc/Bio/DB.html",
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+ "doc/Bio/DB/FastaLengthDB.html",
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  "doc/Bio/DB/Pileup.html",
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  "doc/Bio/DB/Vcf.html",
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  "doc/Bio/Util.html",
@@ -83,13 +84,16 @@ Gem::Specification.new do |s|
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  "doc/rdoc.css",
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  "doc/table_of_contents.html",
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  "examples/.DS_Store",
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+ "examples/Chr1.html",
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+ "examples/gngm_qtl_mapping_HTML_maker_set_options.rb",
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  "examples/make_histograms.rb",
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  "examples/make_threads.rb",
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  "examples/make_threads_isize.rb",
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+ "examples/pileup.txt",
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+ "examples/snps.vcf",
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  "examples/use_indels.rb",
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  "lib/bio-gngm.rb",
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  "lib/bio/util/bio-gngm.rb",
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- "lib/bio/util/mutation_effects.rb",
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  "scripts/get_subseq.rb",
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  "scripts/make_histograms_laerfyve.rb",
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  "scripts/make_histograms_laerfyve_stitched.rb",
data/doc/Bio.html CHANGED
@@ -4,7 +4,7 @@
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  <head>
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  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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- <title>Module: Bio</title>
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+ <title>module Bio - RDoc Documentation</title>
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@@ -81,6 +81,8 @@
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  <li><a href="./Bio/DB.html">Bio::DB</a>
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+ <li><a href="./Bio/DB/FastaLengthDB.html">Bio::DB::FastaLengthDB</a>
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  <li><a href="./Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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  <li><a href="./Bio/DB/Vcf.html">Bio::DB::Vcf</a>
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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 by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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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.html CHANGED
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- <title>Module: Bio::DB</title>
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+ <title>module Bio::DB - RDoc Documentation</title>
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@@ -80,6 +80,8 @@
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  <li><a href="../Bio/DB.html">Bio::DB</a>
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+ <li><a href="../Bio/DB/FastaLengthDB.html">Bio::DB::FastaLengthDB</a>
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  <li><a href="../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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@@ -122,7 +124,7 @@
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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 by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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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/FastaLengthDB.html ADDED
@@ -0,0 +1,238 @@
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+ <!DOCTYPE html>
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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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+ <title>class Bio::DB::FastaLengthDB - RDoc Documentation</title>
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+ <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "../../";
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+ </script>
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+
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+ <script type="text/javascript" charset="utf-8" src="../../js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/search.js"></script>
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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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+
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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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+ </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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+ <ul class="link-list">
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+
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+ <li><a href="#method-c-new">::new</a>
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+
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+ <li><a href="#method-i-each">#each</a>
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+
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+ </ul>
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+ </nav>
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+
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+ </div>
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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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+ <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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+ <li><a href="../../Bio/DB/FastaLengthDB.html">Bio::DB::FastaLengthDB</a>
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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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+
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+ </ul>
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+ </nav>
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+ </div>
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+ </nav>
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+
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+ <div id="documentation">
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+ <h1 class="class">class Bio::DB::FastaLengthDB</h1>
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+
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+ <div id="description" class="description">
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+
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+ <p>Simple class representing a file of Fasta format sequences and each ones
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+ length</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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+
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+
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+
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+
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+
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+ <!-- Methods -->
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+
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+ <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Class Methods</h3>
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+
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+
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+ <div id="method-c-new" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">new</span><span
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+ class="method-args">(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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+ <div class="method-source-code" id="new-source">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 20</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
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+ <span class="ruby-ivar">@file</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:file</span>]
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+ <span class="ruby-ivar">@seqs</span> = {}
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+ <span class="ruby-identifier">file</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">FastaFormat</span>.<span class="ruby-identifier">open</span>(<span class="ruby-ivar">@file</span>)
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+ <span class="ruby-identifier">file</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">entry</span><span class="ruby-operator">|</span>
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+ <span class="ruby-ivar">@seqs</span>[<span class="ruby-identifier">entry</span>.<span class="ruby-identifier">entry_id</span>] = <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">length</span>
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+ <span class="ruby-keyword">end</span>
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+
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">each</span>
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+ <span class="ruby-ivar">@seqs</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">sort</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
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+ <span class="ruby-keyword">yield</span> <span class="ruby-identifier">k</span>, <span class="ruby-ivar">@seqs</span>[<span class="ruby-identifier">k</span>]
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+ <span class="ruby-keyword">end</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><!-- new-source -->
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+ </div>
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+ </div><!-- new-method -->
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+ </section><!-- public-class-method-details -->
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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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+ <div id="method-i-each" class="method-detail ">
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+ <div class="method-heading">
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+ <span class="method-name">each</span><span
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+ class="method-args">() { |k, seqs| ... }</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 28</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">each</span>
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+ <span class="ruby-ivar">@seqs</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">sort</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
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+ <span class="ruby-keyword">yield</span> <span class="ruby-identifier">k</span>, <span class="ruby-ivar">@seqs</span>[<span class="ruby-identifier">k</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><!-- each-source -->
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+ </div><!-- each-method -->
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+ </section><!-- public-instance-method-details -->
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+ </section><!-- 5Buntitled-5D -->
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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> 3.12.
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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/Pileup.html CHANGED
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@@ -99,6 +99,8 @@
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@@ -227,7 +229,7 @@ is compared to the next most common base after it.
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">discordant_chastity</span>
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@@ -282,13 +284,12 @@ reference base is N or n if <code>:ignore_reference_n</code> is set to true</p>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_snp?</span>(<span class="ruby-identifier">opts</span>)
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- <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">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>]
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+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">'*'</span>
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+ <span class="ruby-comment">#return false unless is_ct</span>
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+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span> <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">true</span> <span class="ruby-keyword">if</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>]
292
293
  <span class="ruby-keyword">false</span>
293
294
  <span class="ruby-keyword">end</span></pre>
294
295
  </div><!-- is_snp-3F-source -->
@@ -310,7 +311,7 @@ reference base is N or n if <code>:ignore_reference_n</code> is set to true</p>
310
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311
312
  <footer id="validator-badges">
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313
  <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 by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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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 CHANGED
@@ -4,7 +4,7 @@
4
4
  <head>
5
5
  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
6
6
 
7
- <title>Class: Bio::DB::Vcf</title>
7
+ <title>class Bio::DB::Vcf - RDoc Documentation</title>
8
8
 
9
9
  <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
10
10
 
@@ -74,13 +74,11 @@
74
74
 
75
75
  <li><a href="#method-i-gq">#gq</a>
76
76
 
77
- <li><a href="#method-i-has_just_one_variant-3F">#has_just_one_variant?</a>
78
-
79
- <li><a href="#method-i-is_deletion-3F">#is_deletion?</a>
80
-
81
77
  <li><a href="#method-i-is_indel-3F">#is_indel?</a>
82
78
 
83
- <li><a href="#method-i-is_insertion-3F">#is_insertion?</a>
79
+ <li><a href="#method-i-is_mnp-3F">#is_mnp?</a>
80
+
81
+ <li><a href="#method-i-is_snp-3F">#is_snp?</a>
84
82
 
85
83
  <li><a href="#method-i-mq">#mq</a>
86
84
 
@@ -123,6 +121,8 @@
123
121
 
124
122
  <li><a href="../../Bio/DB.html">Bio::DB</a>
125
123
 
124
+ <li><a href="../../Bio/DB/FastaLengthDB.html">Bio::DB::FastaLengthDB</a>
125
+
126
126
  <li><a href="../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
127
127
 
128
128
  <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
@@ -198,7 +198,7 @@ attribute string on commas</p>
198
198
 
199
199
 
200
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>
201
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 123</span>
202
202
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">alternatives</span>
203
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
204
  <span class="ruby-keyword">end</span></pre>
@@ -230,7 +230,7 @@ href="Vcf.html">Vcf</a> only.</p>
230
230
 
231
231
 
232
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>
233
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 146</span>
234
234
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">gq</span>
235
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
236
  <span class="ruby-keyword">end</span></pre>
@@ -244,41 +244,42 @@ href="Vcf.html">Vcf</a> only.</p>
244
244
  </div><!-- gq-method -->
245
245
 
246
246
 
247
- <div id="method-i-has_just_one_variant-3F" class="method-detail ">
247
+ <div id="method-i-is_indel-3F" class="method-detail ">
248
248
 
249
249
  <div class="method-heading">
250
- <span class="method-name">has_just_one_variant?</span><span
251
- class="method-args">()</span>
250
+ <span class="method-name">is_indel?</span><span
251
+ class="method-args">(options)</span>
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252
  <span class="method-click-advice">click to toggle source</span>
253
253
  </div>
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254
 
255
255
 
256
256
  <div class="method-description">
257
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>
258
+ <p>Returns true if ref col is different in length from any of the entries in
259
+ alt column</p>
260
260
 
261
261
 
262
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>
263
+ <div class="method-source-code" id="is_indel-3F-source">
264
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 186</span>
265
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_indel?</span>(<span class="ruby-identifier">options</span>)
266
+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">variant?</span> <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alternatives</span>.<span class="ruby-identifier">any?</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">!=</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>)
267
+ <span class="ruby-keyword">false</span>
267
268
  <span class="ruby-keyword">end</span></pre>
268
- </div><!-- has_just_one_variant-3F-source -->
269
+ </div><!-- is_indel-3F-source -->
269
270
 
270
271
  </div>
271
272
 
272
273
 
273
274
 
274
275
 
275
- </div><!-- has_just_one_variant-3F-method -->
276
+ </div><!-- is_indel-3F-method -->
276
277
 
277
278
 
278
- <div id="method-i-is_deletion-3F" class="method-detail ">
279
+ <div id="method-i-is_mnp-3F" class="method-detail ">
279
280
 
280
281
  <div class="method-heading">
281
- <span class="method-name">is_deletion?</span><span
282
+ <span class="method-name">is_mnp?</span><span
282
283
  class="method-args">(options)</span>
283
284
  <span class="method-click-advice">click to toggle source</span>
284
285
  </div>
@@ -286,107 +287,56 @@ one allele are too complicated for now, so are discarded…</p>
286
287
 
287
288
  <div class="method-description">
288
289
 
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>
290
+ <p>returns true if ref col has same length as all alternatives and position
291
+ variant passes quality</p>
295
292
 
296
293
 
297
294
 
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>
295
+ <div class="method-source-code" id="is_mnp-3F-source">
296
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 174</span>
297
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_mnp?</span>(<span class="ruby-identifier">options</span>)
298
+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alternatives</span>.<span class="ruby-identifier">all?</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</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>)
307
299
  <span class="ruby-keyword">false</span>
308
300
  <span class="ruby-keyword">end</span></pre>
309
- </div><!-- is_deletion-3F-source -->
301
+ </div><!-- is_mnp-3F-source -->
310
302
 
311
303
  </div>
312
304
 
313
305
 
314
306
 
315
307
 
316
- </div><!-- is_deletion-3F-method -->
308
+ </div><!-- is_mnp-3F-method -->
317
309
 
318
310
 
319
- <div id="method-i-is_indel-3F" class="method-detail ">
311
+ <div id="method-i-is_snp-3F" class="method-detail ">
320
312
 
321
313
  <div class="method-heading">
322
- <span class="method-name">is_indel?</span><span
323
- class="method-args">(opts)</span>
314
+ <span class="method-name">is_snp?</span><span
315
+ class="method-args">(options)</span>
324
316
  <span class="method-click-advice">click to toggle source</span>
325
317
  </div>
326
318
 
327
319
 
328
320
  <div class="method-description">
329
321
 
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>
322
+ <p>returns true if ref col has length of 1 and is_mnp?</p>
333
323
 
334
324
 
335
325
 
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>
377
- <span class="ruby-keyword">else</span> <span class="ruby-keyword">false</span>
378
- <span class="ruby-keyword">end</span>
379
- <span class="ruby-keyword">rescue</span> <span class="ruby-comment">## if something goes wrong, skip the postion, </span>
380
- <span class="ruby-keyword">false</span>
326
+ <div class="method-source-code" id="is_snp-3F-source">
327
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 180</span>
328
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_snp?</span>(<span class="ruby-identifier">options</span>)
329
+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">is_mnp?</span>(<span class="ruby-identifier">options</span>) <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span>
330
+ <span class="ruby-keyword">false</span>
381
331
  <span class="ruby-keyword">end</span></pre>
382
- </div><!-- is_insertion-3F-source -->
332
+ </div><!-- is_snp-3F-source -->
383
333
 
384
334
  </div>
385
335
 
386
336
 
387
337
 
388
338
 
389
- </div><!-- is_insertion-3F-method -->
339
+ </div><!-- is_snp-3F-method -->
390
340
 
391
341
 
392
342
  <div id="method-i-mq" class="method-detail ">
@@ -406,7 +356,7 @@ defined by the <a href="Vcf.html">Vcf</a> MQ attribute.</p>
406
356
 
407
357
 
408
358
  <div class="method-source-code" id="mq-source">
409
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 119</span>
359
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 141</span>
410
360
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">mq</span>
411
361
  <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>
412
362
  <span class="ruby-keyword">end</span></pre>
@@ -437,7 +387,7 @@ of the last two figures in the DP4 attribute.</p>
437
387
 
438
388
 
439
389
  <div class="method-source-code" id="non_ref_allele_count-source">
440
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 106</span>
390
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 128</span>
441
391
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">non_ref_allele_count</span>
442
392
  <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>
443
393
  <span class="ruby-keyword">end</span></pre>
@@ -472,7 +422,7 @@ the genotype call,</p>
472
422
 
473
423
 
474
424
  <div class="method-source-code" id="non_ref_allele_freq-source">
475
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 114</span>
425
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 136</span>
476
426
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">non_ref_allele_freq</span>
477
427
  <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>
478
428
  <span class="ruby-keyword">end</span></pre>
@@ -510,15 +460,15 @@ the genotype call,</p>
510
460
 
511
461
  <p>Example</p>
512
462
 
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>)
463
+ <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>, :<span class="ruby-identifier">min_snp_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">20</span>)
514
464
  </pre>
515
465
 
516
466
 
517
467
 
518
468
  <div class="method-source-code" id="pass_quality-3F-source">
519
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 147</span>
469
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 169</span>
520
470
  <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">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>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">qual</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:min_snp_quality</span>])
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  <span class="ruby-keyword">end</span></pre>
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  </div><!-- pass_quality-3F-source -->
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@@ -548,7 +498,7 @@ sample in the <a href="Vcf.html">Vcf</a> only.</p>
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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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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 151</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>
@@ -580,7 +530,7 @@ href="Vcf.html">Vcf</a> object.</p>
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  <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>
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 107</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_s</span>
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  <span class="ruby-node">&quot;#{self.chrom} #{self.pos} #{self.ref} #{self.alt} #{self.info}&quot;</span>
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  <span class="ruby-keyword">end</span></pre>
@@ -611,7 +561,7 @@ of the DP4 attribute. Returns 0.0 if no value is calculated.</p>
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  <div class="method-source-code" id="used_depth-source">
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- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 90</span>
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 112</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">used_depth</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-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>
@@ -654,7 +604,7 @@ href="Vcf.html">Vcf</a> is not <strong>.</strong></p>
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  <div class="method-source-code" id="variant-3F-source">
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- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 80</span>
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 102</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">variant?</span>
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  <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>
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  <span class="ruby-keyword">end</span></pre>
@@ -677,7 +627,7 @@ href="Vcf.html">Vcf</a> is not <strong>.</strong></p>
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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 by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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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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