parse_fasta 1.0.0 → 1.0.1

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Files changed (22) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +1 -0
  3. data/lib/parse_fasta/version.rb +1 -1
  4. metadata +1 -19
  5. data/doc/FastaFile.html +0 -292
  6. data/doc/File.html +0 -212
  7. data/doc/ParseFasta.html +0 -144
  8. data/doc/Sequence.html +0 -361
  9. data/doc/_index.html +0 -136
  10. data/doc/class_list.html +0 -54
  11. data/doc/css/common.css +0 -1
  12. data/doc/css/full_list.css +0 -57
  13. data/doc/css/style.css +0 -339
  14. data/doc/file.README.html +0 -161
  15. data/doc/file_list.html +0 -56
  16. data/doc/frames.html +0 -26
  17. data/doc/index.html +0 -161
  18. data/doc/js/app.js +0 -219
  19. data/doc/js/full_list.js +0 -178
  20. data/doc/js/jquery.js +0 -4
  21. data/doc/method_list.html +0 -71
  22. data/doc/top-level-namespace.html +0 -114
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@@ -1,7 +1,7 @@
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+ data.tar.gz: d1bf3eb669efe8d5747315315b1cbb7370d70ed0614e64ea44beb9fd08990554e4609364ce623a54e896e74becd222c124da92ff5a716acfccc55b9887f5cf24
data/.gitignore CHANGED
@@ -6,6 +6,7 @@
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  Gemfile.lock
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  InstalledFiles
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  _yardoc
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+ doc/
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  coverage
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  lib/bundler/man
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  pkg
data/lib/parse_fasta/version.rb CHANGED
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  # along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
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  module ParseFasta
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- VERSION = "1.0.0"
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+ VERSION = "1.0.1"
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: parse_fasta
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  version: !ruby/object:Gem::Version
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- version: 1.0.0
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+ version: 1.0.1
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  platform: ruby
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  authors:
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  - Ryan Moore
@@ -92,24 +92,6 @@ files:
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  - Gemfile
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  - README.md
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  - Rakefile
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- - doc/FastaFile.html
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- - doc/File.html
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- - doc/ParseFasta.html
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- - doc/Sequence.html
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- - doc/_index.html
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- - doc/class_list.html
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- - doc/css/common.css
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- - doc/css/full_list.css
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- - doc/css/style.css
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- - doc/file.README.html
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- - doc/file_list.html
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- - doc/frames.html
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- - doc/index.html
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- - doc/js/app.js
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- - doc/js/full_list.js
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- - doc/js/jquery.js
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- - doc/method_list.html
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- - doc/top-level-namespace.html
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  - lib/parse_fasta.rb
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  - lib/parse_fasta/fasta_file.rb
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  - lib/parse_fasta/sequence.rb
data/doc/FastaFile.html DELETED
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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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- &mdash; Documentation by YARD 0.8.7.4
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- </title>
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- <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
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- <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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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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- <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/app.js"></script>
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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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- <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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- <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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- <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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- </div>
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- <div class="clear"></div>
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- </div>
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- <iframe id="search_frame"></iframe>
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- <div id="content"><h1>Class: FastaFile
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- </h1>
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-
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- <dl class="box">
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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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- <ul class="fullTree">
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- <li>Object</li>
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- <li class="next">File</li>
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- </dd>
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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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- </dl>
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- <div class="clear"></div>
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- <h2>Overview</h2><div class="docstring">
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- <div class="discussion">
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- <p>Provides simple interface for parsing fasta format files.</p>
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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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- <ul class="summary">
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- <li class="public ">
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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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- - (<tt>Object</tt>) <strong>each_record</strong> {|header, sequence| ... }
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- </h3><div class="docstring">
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- <div class="discussion">
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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>
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- <div class="tags">
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- <div class="examples">
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- <p class="tag_title">Examples:</p>
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- <p>Parsing a fasta file</p>
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- </div></p>
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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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- </div>
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- <p class="tag_title">Yields:</p>
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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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- Generated on Tue Jun 3 22:55:41 2014 by
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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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- </table>
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- </div>
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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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- </html>