parse_fasta 0.0.5 → 1.0.0

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Files changed (36) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +0 -1
  3. data/COPYING +674 -0
  4. data/README.md +56 -6
  5. data/Rakefile +6 -0
  6. data/doc/FastaFile.html +292 -0
  7. data/doc/File.html +212 -0
  8. data/doc/ParseFasta.html +144 -0
  9. data/doc/Sequence.html +361 -0
  10. data/doc/_index.html +136 -0
  11. data/doc/class_list.html +54 -0
  12. data/doc/css/common.css +1 -0
  13. data/doc/css/full_list.css +57 -0
  14. data/doc/css/style.css +339 -0
  15. data/doc/file.README.html +161 -0
  16. data/doc/file_list.html +56 -0
  17. data/doc/frames.html +26 -0
  18. data/doc/index.html +161 -0
  19. data/doc/js/app.js +219 -0
  20. data/doc/js/full_list.js +178 -0
  21. data/doc/js/jquery.js +4 -0
  22. data/doc/method_list.html +71 -0
  23. data/doc/top-level-namespace.html +114 -0
  24. data/lib/parse_fasta/fasta_file.rb +46 -0
  25. data/lib/parse_fasta/sequence.rb +55 -0
  26. data/lib/parse_fasta/version.rb +19 -1
  27. data/lib/parse_fasta.rb +11 -21
  28. data/parse_fasta.gemspec +3 -0
  29. data/spec/lib/fasta_file_spec.rb +46 -0
  30. data/spec/lib/sequence_spec.rb +52 -0
  31. data/spec/spec_helper.rb +19 -0
  32. data/test_files/benchmark.rb +70 -0
  33. data/test_files/test.fa +9 -0
  34. metadata +75 -5
  35. data/LICENSE.txt +0 -22
  36. data/benchmark.rb +0 -22
data/README.md CHANGED
@@ -18,16 +18,36 @@ Or install it yourself as:
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  ## Overview ##
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- Provides the method `#each_record` for the `File` class.
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+ I wanted a simple, fast way to parse fasta files so I wouldn't have to
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+ keep writing annoying boilerplate fasta parsing code everytime I go to
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+ do something with one. I will probably add more, but likely only tasks
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+ that I find myself doing over and over.
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- each_record { |header, sequence| block }
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+ ## Usage ##
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- The whole file is not loaded into memory, so have no fear of giant
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- fasta files!
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+ ### Version 1.0.0 (current) ###
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- ## Usage ##
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+ The monkey patch of the `File` class is no more! Here is the new print
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+ length example:
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+
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+ require 'parse_fasta'
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+
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+ FastaFile.open(ARGV.first, 'r').each_record do |header, sequence|
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+ puts [header, sequence.length].join("\t")
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+ end
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+
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+ And here, a script to calculate GC content:
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+
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+ require 'parse_fasta'
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+
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+ FastaFile.open(ARGV.first, 'r').each_record do |header, sequence|
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+ puts [header, sequence.gc].join("\t")
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+ end
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+
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+ ### Version 0.0.5 (old) ###
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- An example that lists the length for each sequence.
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+ An example that lists the length for each sequence. (Won't work in
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+ version 1.0.0)
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  require 'parse_fasta'
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@@ -37,6 +57,12 @@ An example that lists the length for each sequence.
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  ## Benchmark ##
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+ Take these with a grain of salt since `BioRuby` is a heavy weight
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+ module with lots of features and error checking, whereas `parse_fasta`
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+ is meant to be lightweight and easy to use for my own coding.
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+
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+ ### FastaFile#each_record ###
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+
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  Just for fun, I wanted to compare the execution time to that of
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  BioRuby. I calculated sequence length for each fasta record with both
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  the `each_record` method from this gem and using the `FastaFormat`
@@ -52,6 +78,30 @@ was 1.1 gigabytes. Here are the results from Ruby's `Benchmark` class:
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  I just wanted a nice, clean way to parse fasta files, but being nearly
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  twice as fasta as BioRuby doesn't hurt either!
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+ ### Sequence#gc ###
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+
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+ I played around with a few different implementations for the `#gc`
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+ method and found this one to be the fastest.
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+
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+ The test is done one random strings mating `/[AaCcTtGgUu]/`. `this_gc`
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+ is `Sequence.new(str).gc`, and `bioruby_gc` is
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+ `Bio::Sequence::NA.new(str).gc_content`.
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+
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+ To see how the methods scale, the test 1 string was 2,000,000 bases,
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+ test 2 was 4,000,000 and test 3 was 8,000,000 bases.
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+
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+ user system total real
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+ this_gc 1 0.030000 0.000000 0.030000 ( 0.029145)
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+ bioruby_gc 1 2.030000 0.010000 2.040000 ( 2.157512)
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+
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+ this_gc 2 0.060000 0.000000 0.060000 ( 0.059408)
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+ bioruby_gc 2 4.060000 0.020000 4.080000 ( 4.334159)
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+
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+ this_gc 3 0.120000 0.000000 0.120000 ( 0.185434)
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+ bioruby_gc 3 8.060000 0.020000 8.080000 ( 8.659071)
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+
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+ Nice!
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+
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  ## Notes ##
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  Currently in doesn't check whether your file is actually a fasta file
data/Rakefile CHANGED
@@ -1,2 +1,8 @@
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  require "bundler/gem_tasks"
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+ require "rspec/core/rake_task"
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+
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+ RSpec::Core::RakeTask.new
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+
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+ task default: :spec
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+ task test: :spec
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data/doc/FastaFile.html ADDED
@@ -0,0 +1,292 @@
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ Class: FastaFile
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+
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+ &mdash; Documentation by YARD 0.8.7.4
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+
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+ </title>
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+
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+ <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
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+
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+ <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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+
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+ <script type="text/javascript" charset="utf-8">
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+ hasFrames = window.top.frames.main ? true : false;
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+ relpath = '';
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+ framesUrl = "frames.html#!FastaFile.html";
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+ </script>
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+
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+
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+ <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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+
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+ <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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+
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+
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+ </head>
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+ <body>
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+ <div id="header">
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+ <div id="menu">
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+
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+ <a href="_index.html">Index (F)</a> &raquo;
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+
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+
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+ <span class="title">FastaFile</span>
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+
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+
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ </div>
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+
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+ <div id="search">
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+
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+ <a class="full_list_link" id="class_list_link"
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+ href="class_list.html">
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+ Class List
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+ </a>
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+
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+ <a class="full_list_link" id="method_list_link"
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+ href="method_list.html">
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+ Method List
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+ </a>
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+
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+ <a class="full_list_link" id="file_list_link"
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+ href="file_list.html">
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+ File List
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+ </a>
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+
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+ </div>
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+ <div class="clear"></div>
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+ </div>
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+
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><h1>Class: FastaFile
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+
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+
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+
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+ </h1>
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+
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+ <dl class="box">
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+
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+ <dt class="r1">Inherits:</dt>
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+ <dd class="r1">
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+ <span class="inheritName">File</span>
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+
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+ <ul class="fullTree">
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+ <li>Object</li>
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+
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+ <li class="next">File</li>
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+
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+ <li class="next">FastaFile</li>
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+
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+ </ul>
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+ <a href="#" class="inheritanceTree">show all</a>
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+
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+ </dd>
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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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+
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+ <dt class="r2 last">Defined in:</dt>
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+ <dd class="r2 last">lib/parse_fasta/fasta_file.rb</dd>
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+
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+ </dl>
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+ <div class="clear"></div>
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+
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+ <h2>Overview</h2><div class="docstring">
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+ <div class="discussion">
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+
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+ <p>Provides simple interface for parsing fasta format files.</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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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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+
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+
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+
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+ <h2>
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+ Instance Method Summary
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+ <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
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+ </h2>
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+
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+ <ul class="summary">
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#each_record-instance_method" title="#each_record (instance method)">- (Object) <strong>each_record</strong> {|header, sequence| ... }</a>
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+
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+
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+
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+ </span>
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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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+
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+ <span class="summary_desc"><div class='inline'>
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+ <p>Analagous to File#each_line, #each_record is used to go through a fasta
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+ file record by record.</p>
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+ </div></span>
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+
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+ </li>
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+
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+
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+ </ul>
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+
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+
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+
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+
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+
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+ <div id="instance_method_details" class="method_details_list">
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+ <h2>Instance Method Details</h2>
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+
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+
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+ <div class="method_details first">
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+ <h3 class="signature first" id="each_record-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>each_record</strong> {|header, sequence| ... }
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+
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+ <p>Analagous to File#each_line, #each_record is used to go through a fasta
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+ file record by record.</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+ <div class="examples">
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+ <p class="tag_title">Examples:</p>
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+
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+
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+ <p class="example_title"><div class='inline'>
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+ <p>Parsing a fasta file</p>
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+ </div></p>
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+
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+ <pre class="example code"><code><span class='const'>FastaFile</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>reads.fna</span><span class='tstring_end'>&#39;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>r</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_record'>each_record</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span>
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+ <span class='id identifier rubyid_puts'>puts</span> <span class='lbracket'>[</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='period'>.</span><span class='id identifier rubyid_gc'>gc</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\t</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></code></pre>
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+
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+ </div>
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+
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+ <p class="tag_title">Yields:</p>
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+ <ul class="yield">
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+
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+ <li>
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+
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+
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+ <span class='type'></span>
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+
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+
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+
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+
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+ <div class='inline'>
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+ <p>The header and sequence for each record in the fasta file to the block</p>
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+ </div>
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+
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+ </li>
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+
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+ </ul>
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+ <p class="tag_title">Yield Parameters:</p>
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+ <ul class="yieldparam">
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+
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+ <li>
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+
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+ <span class='name'>header</span>
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+
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+
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+ <span class='type'>(<tt>String</tt>)</span>
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+
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+
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+
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+ &mdash;
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+ <div class='inline'>
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+ <p>The header of the fasta record without the leading &#39;&gt;&#39;</p>
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+ </div>
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+
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+ </li>
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+
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+ <li>
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+
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+ <span class='name'>sequence</span>
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+
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+
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+ <span class='type'>(<tt><span class='object_link'><a href="Sequence.html" title="Sequence (class)">Sequence</a></span></tt>)</span>
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+
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+
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+
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+ &mdash;
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+ <div class='inline'>
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+ <p>The sequence of the fasta record</p>
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+ </div>
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+
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+ </li>
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+
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+ </ul>
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 35
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+ 36
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+ 37
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+ 38
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+ 39
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+ 40</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/parse_fasta/fasta_file.rb', line 35</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_each_record'>each_record</span>
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+ <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n&gt;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_line'>line</span><span class='op'>|</span>
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+ <span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span> <span class='op'>=</span> <span class='id identifier rubyid_parse_line'>parse_line</span><span class='lparen'>(</span><span class='id identifier rubyid_line'>line</span><span class='rparen'>)</span>
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+ <span class='kw'>yield</span><span class='lparen'>(</span><span class='id identifier rubyid_header'>header</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='comma'>,</span> <span class='const'>Sequence</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_sequence'>sequence</span><span class='rparen'>)</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+ </div>
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+
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+ <div id="footer">
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+ Generated on Tue Jun 3 22:55:41 2014 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.8.7.4 (ruby-2.1.1).
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/File.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ Class: File
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+
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+ &mdash; Documentation by YARD 0.8.7.4
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+
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+ </title>
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+
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+ <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
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+
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+ <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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+
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+ <script type="text/javascript" charset="utf-8">
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+ hasFrames = window.top.frames.main ? true : false;
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+ relpath = '';
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+ framesUrl = "frames.html#!File.html";
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+ </script>
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+
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+
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+ <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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+
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+ <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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+
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+
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+ </head>
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+ <body>
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+ <div id="header">
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+ <div id="menu">
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+
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+ <a href="_index.html">Index (F)</a> &raquo;
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+
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+
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+ <span class="title">File</span>
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+
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+
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ </div>
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+
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+ <div id="search">
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+
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+ <a class="full_list_link" id="class_list_link"
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+ href="class_list.html">
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+ Class List
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+ </a>
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+
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+ <a class="full_list_link" id="method_list_link"
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+ href="method_list.html">
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+ Method List
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+ </a>
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+
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+ <a class="full_list_link" id="file_list_link"
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+ href="file_list.html">
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+ File List
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+ </a>
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+
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+ </div>
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+ <div class="clear"></div>
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+ </div>
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+
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><h1>Class: File
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+
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+
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+
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+ </h1>
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+
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+ <dl class="box">
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+
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+ <dt class="r1">Inherits:</dt>
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+ <dd class="r1">
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+ <span class="inheritName">Object</span>
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+
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+ <ul class="fullTree">
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+ <li>Object</li>
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+
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+ <li class="next">File</li>
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+
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+ </ul>
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+ <a href="#" class="inheritanceTree">show all</a>
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+
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+ </dd>
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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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+ <dt class="r2 last">Defined in:</dt>
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+ <dd class="r2 last">lib/parse_fasta/file.rb</dd>
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+
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+ </dl>
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+ <div class="clear"></div>
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+
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+ <h2>Overview</h2><div class="docstring">
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+ <div class="discussion">
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+
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+ <p>You should have received a copy of the GNU General Public License along
106
+ with parse_fasta. If not, see &lt;<a
107
+ href="http://www.gnu.org/licenses">www.gnu.org/licenses</a>/&gt;.</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ </div><div id="subclasses">
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+ <h2>Direct Known Subclasses</h2>
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+ <p class="children"><span class='object_link'><a href="FastaFile.html" title="FastaFile (class)">FastaFile</a></span></p>
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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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+
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+
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+
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+
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+ <h2>
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+ Instance Method Summary
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+ <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
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+ </h2>
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+
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+ <ul class="summary">
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#each_record-instance_method" title="#each_record (instance method)">- (Object) <strong>each_record</strong> </a>
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+
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+
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+
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+ </span>
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'></div></span>
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+
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+ </li>
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+
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+
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+ </ul>
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+
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+
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+
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+
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+ <div id="instance_method_details" class="method_details_list">
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+ <h2>Instance Method Details</h2>
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+
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+
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+ <div class="method_details first">
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+ <h3 class="signature first" id="each_record-instance_method">
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+
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+ - (<tt>Object</tt>) <strong>each_record</strong>
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+
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+
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+
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+ </h3><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+ 20
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+ 21
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+ 22
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+ 23
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+ 24
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+ 25</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/parse_fasta/file.rb', line 20</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_each_record'>each_record</span>
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+ <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n&gt;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_line'>line</span><span class='op'>|</span>
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+ <span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span> <span class='op'>=</span> <span class='id identifier rubyid_parse_line'>parse_line</span><span class='lparen'>(</span><span class='id identifier rubyid_line'>line</span><span class='rparen'>)</span>
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+ <span class='kw'>yield</span> <span class='id identifier rubyid_header'>header</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span>
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+ <span class='kw'>end</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+ </div>
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+
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+ <div id="footer">
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+ Generated on Tue Jun 3 22:41:14 2014 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.8.7.4 (ruby-2.1.1).
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+ </div>
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+
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+ </body>
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+ </html>