parse_fasta 0.0.5 → 1.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (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/doc/class_list.html ADDED
@@ -0,0 +1,54 @@
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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>
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+ <head>
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+
7
+ <link rel="stylesheet" href="css/full_list.css" type="text/css" media="screen" charset="utf-8" />
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+
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+ <link rel="stylesheet" href="css/common.css" type="text/css" media="screen" charset="utf-8" />
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+
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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/full_list.js"></script>
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+
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+
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+ <title>Class List</title>
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+ <base id="base_target" target="_parent" />
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+ </head>
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+ <body>
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+ <script type="text/javascript" charset="utf-8">
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+ if (window.top.frames.main) {
24
+ document.getElementById('base_target').target = 'main';
25
+ document.body.className = 'frames';
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+ }
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+ </script>
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+ <div id="content">
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+ <h1 id="full_list_header">Class List</h1>
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+ <div id="nav">
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+
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+ <span><a target="_self" href="class_list.html">
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+ Classes
34
+ </a></span>
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+
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+ <span><a target="_self" href="method_list.html">
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+ Methods
38
+ </a></span>
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+
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+ <span><a target="_self" href="file_list.html">
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+ Files
42
+ </a></span>
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+
44
+ </div>
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+ <div id="search">Search: <input type="text" /></div>
46
+
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+ <ul id="full_list" class="class">
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+ <li><span class='object_link'><a href="top-level-namespace.html" title="Top Level Namespace (root)">Top Level Namespace</a></span></li>
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+ <li><span class='object_link'><a href="FastaFile.html" title="FastaFile (class)">FastaFile</a></span> &lt; File<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="ParseFasta.html" title="ParseFasta (module)">ParseFasta</a></span><small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="Sequence.html" title="Sequence (class)">Sequence</a></span> &lt; String<small class='search_info'>Top Level Namespace</small></li>
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+
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+ </ul>
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+ </div>
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+ </body>
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+ </html>
data/doc/css/common.css ADDED
@@ -0,0 +1 @@
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+ /* Override this file with custom rules */
data/doc/css/full_list.css ADDED
@@ -0,0 +1,57 @@
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+ body {
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+ margin: 0;
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+ font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif;
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+ font-size: 13px;
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+ height: 101%;
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+ overflow-x: hidden;
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+ }
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+
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+ h1 { padding: 12px 10px; padding-bottom: 0; margin: 0; font-size: 1.4em; }
10
+ .clear { clear: both; }
11
+ #search { position: absolute; right: 5px; top: 9px; padding-left: 24px; }
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+ #content.insearch #search, #content.insearch #noresults { background: url(data:image/gif;base64,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) no-repeat center left; }
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+ #full_list { padding: 0; list-style: none; margin-left: 0; }
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+ #full_list ul { padding: 0; }
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+ #full_list li { padding: 5px; padding-left: 12px; margin: 0; font-size: 1.1em; list-style: none; }
16
+ #noresults { padding: 7px 12px; }
17
+ #content.insearch #noresults { margin-left: 7px; }
18
+ ul.collapsed ul, ul.collapsed li { display: none; }
19
+ ul.collapsed.search_uncollapsed { display: block; }
20
+ ul.collapsed.search_uncollapsed li { display: list-item; }
21
+ li a.toggle { cursor: default; position: relative; left: -5px; top: 4px; text-indent: -999px; width: 10px; height: 9px; margin-left: -10px; display: block; float: left; background: url(data:image/png;base64,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) no-repeat bottom left; }
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+ li.collapsed a.toggle { opacity: 0.5; cursor: default; background-position: top left; }
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+ li { color: #888; cursor: pointer; }
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+ li.deprecated { text-decoration: line-through; font-style: italic; }
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+ li.r1 { background: #f0f0f0; }
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+ li.r2 { background: #fafafa; }
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+ li:hover { background: #ddd; }
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+ li small:before { content: "("; }
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+ li small:after { content: ")"; }
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+ li small.search_info { display: none; }
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+ a:link, a:visited { text-decoration: none; color: #05a; }
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+ li.clicked { background: #05a; color: #ccc; }
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+ li.clicked a:link, li.clicked a:visited { color: #eee; }
34
+ li.clicked a.toggle { opacity: 0.5; background-position: bottom right; }
35
+ li.collapsed.clicked a.toggle { background-position: top right; }
36
+ #search input { border: 1px solid #bbb; -moz-border-radius: 3px; -webkit-border-radius: 3px; }
37
+ #nav { margin-left: 10px; font-size: 0.9em; display: none; color: #aaa; }
38
+ #nav a:link, #nav a:visited { color: #358; }
39
+ #nav a:hover { background: transparent; color: #5af; }
40
+ .frames #nav span:after { content: ' | '; }
41
+ .frames #nav span:last-child:after { content: ''; }
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+
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+ .frames #content h1 { margin-top: 0; }
44
+ .frames li { white-space: nowrap; cursor: normal; }
45
+ .frames li small { display: block; font-size: 0.8em; }
46
+ .frames li small:before { content: ""; }
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+ .frames li small:after { content: ""; }
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+ .frames li small.search_info { display: none; }
49
+ .frames #search { width: 170px; position: static; margin: 3px; margin-left: 10px; font-size: 0.9em; color: #888; padding-left: 0; padding-right: 24px; }
50
+ .frames #content.insearch #search { background-position: center right; }
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+ .frames #search input { width: 110px; }
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+ .frames #nav { display: block; }
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+
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+ #full_list.insearch li { display: none; }
55
+ #full_list.insearch li.found { display: list-item; padding-left: 10px; }
56
+ #full_list.insearch li a.toggle { display: none; }
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+ #full_list.insearch li small.search_info { display: block; }
data/doc/css/style.css ADDED
@@ -0,0 +1,339 @@
1
+ body {
2
+ padding: 0 20px;
3
+ font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif;
4
+ font-size: 13px;
5
+ }
6
+ body.frames { padding: 0 5px; }
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+ h1 { font-size: 25px; margin: 1em 0 0.5em; padding-top: 4px; border-top: 1px dotted #d5d5d5; }
8
+ h1.noborder { border-top: 0px; margin-top: 0; padding-top: 4px; }
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+ h1.title { margin-bottom: 10px; }
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+ h1.alphaindex { margin-top: 0; font-size: 22px; }
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+ h2 {
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+ padding: 0;
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+ padding-bottom: 3px;
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+ border-bottom: 1px #aaa solid;
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+ font-size: 1.4em;
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+ margin: 1.8em 0 0.5em;
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+ }
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+ h2 small { font-weight: normal; font-size: 0.7em; display: block; float: right; }
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+ .clear { clear: both; }
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+ .inline { display: inline; }
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+ .inline p:first-child { display: inline; }
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+ .docstring h1, .docstring h2, .docstring h3, .docstring h4 { padding: 0; border: 0; border-bottom: 1px dotted #bbb; }
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+ .docstring h1 { font-size: 1.2em; }
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+ .docstring h2 { font-size: 1.1em; }
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+ .docstring h3, .docstring h4 { font-size: 1em; border-bottom: 0; padding-top: 10px; }
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+ .summary_desc .object_link, .docstring .object_link { font-family: monospace; }
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+ .rdoc-term { padding-right: 25px; font-weight: bold; }
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+ .rdoc-list p { margin: 0; padding: 0; margin-bottom: 4px; }
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+
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+ /* style for <table> */
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+ #filecontents table, .docstring table { border-collapse: collapse; }
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+ #filecontents table th, #filecontents table td,
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+ .docstring table th, .docstring table td { border: 1px solid #ccc; padding: 8px; padding-right: 17px; }
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+ #filecontents table tr:nth-child(odd),
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+ .docstring table tr:nth-child(odd) { background: #eee; }
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+ #filecontents table tr:nth-child(even),
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+ .docstring table tr:nth-child(even) { background: #fff; }
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+ #filecontents table th, .docstring table th { background: #fff; }
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+
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+ /* style for <ul> */
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+ #filecontents li > p, .docstring li > p { margin: 0px; }
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+ #filecontents ul, .docstring ul { padding-left: 20px; }
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+ /* style for <dl> */
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+ #filecontents dl, .docstring dl { border: 1px solid #ccc; }
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+ #filecontents dt, .docstring dt { background: #ddd; font-weight: bold; padding: 3px 5px; }
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+ #filecontents dd, .docstring dd { padding: 5px 0px; margin-left: 18px; }
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+ #filecontents dd > p, .docstring dd > p { margin: 0px; }
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+
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+ .note {
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+ color: #222;
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+ -moz-border-radius: 3px; -webkit-border-radius: 3px;
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+ background: #e3e4e3; border: 1px solid #d5d5d5; padding: 7px 10px;
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+ display: block;
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+ }
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+ .note.todo { background: #ffffc5; border-color: #ececaa; }
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+ .note.returns_void { background: #efefef; }
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+ .note.deprecated { background: #ffe5e5; border-color: #e9dada; }
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+ .note.private { background: #ffffc5; border-color: #ececaa; }
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+ .note.title { padding: 1px 5px; font-size: 0.9em; font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif; display: inline; }
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+ .summary_signature + .note.title { margin-left: 7px; }
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+ h1 .note.title { font-size: 0.5em; font-weight: normal; padding: 3px 5px; position: relative; top: -3px; text-transform: capitalize; }
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+ .note.title.constructor { color: #fff; background: #6a98d6; border-color: #6689d6; }
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+ .note.title.writeonly { color: #fff; background: #45a638; border-color: #2da31d; }
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+ .note.title.readonly { color: #fff; background: #6a98d6; border-color: #6689d6; }
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+ .note.title.private { background: #d5d5d5; border-color: #c5c5c5; }
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+ .note.title.not_defined_here { background: transparent; border: none; font-style: italic; }
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+ .discussion .note { margin-top: 6px; }
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+ .discussion .note:first-child { margin-top: 0; }
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+
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+ h3.inherited {
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+ font-style: italic;
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+ font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif;
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+ font-weight: normal;
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+ padding: 0;
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+ margin: 0;
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+ margin-top: 12px;
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+ margin-bottom: 3px;
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+ font-size: 13px;
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+ }
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+ p.inherited {
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+ padding: 0;
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+ margin: 0;
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+ margin-left: 25px;
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+ }
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+
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+ #filecontents dl.box, dl.box {
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+ border: 0;
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+ width: 520px;
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+ font-size: 1em;
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+ }
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+ #filecontents dl.box dt, dl.box dt {
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+ float: left;
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+ display: block;
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+ width: 100px;
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+ margin: 0;
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+ text-align: right;
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+ font-weight: bold;
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+ background: transparent;
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+ border: 1px solid #aaa;
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+ border-width: 1px 0px 0px 1px;
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+ padding: 6px 0;
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+ padding-right: 10px;
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+ }
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+ #filecontents dl.box dd, dl.box dd {
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+ float: left;
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+ display: block;
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+ width: 380px;
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+ margin: 0;
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+ padding: 6px 0;
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+ padding-right: 20px;
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+ border: 1px solid #aaa;
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+ border-width: 1px 1px 0 0;
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+ }
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+ #filecontents dl.box .last, dl.box .last {
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+ border-bottom: 1px solid #aaa;
116
+ }
117
+ #filecontents dl.box .r1, dl.box .r1 { background: #eee; }
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+
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+ ul.toplevel { list-style: none; padding-left: 0; font-size: 1.1em; }
120
+ .index_inline_list { padding-left: 0; font-size: 1.1em; }
121
+ .index_inline_list li { list-style: none; display: inline; padding: 7px 12px; line-height: 35px; }
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+
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+ dl.constants { margin-left: 40px; }
124
+ dl.constants dt { font-weight: bold; font-size: 1.1em; margin-bottom: 5px; }
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+ dl.constants dd { width: 75%; white-space: pre; font-family: monospace; margin-bottom: 18px; }
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+
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+ .summary_desc { margin-left: 32px; display: block; font-family: sans-serif; }
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+ .summary_desc tt { font-size: 0.9em; }
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+ dl.constants .note { padding: 2px 6px; padding-right: 12px; margin-top: 6px; }
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+ dl.constants .docstring { margin-left: 32px; font-size: 0.9em; font-weight: normal; }
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+ dl.constants .tags { padding-left: 32px; font-size: 0.9em; line-height: 0.8em; }
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+ dl.constants .discussion *:first-child { margin-top: 0; }
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+ dl.constants .discussion *:last-child { margin-bottom: 0; }
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+
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+ .method_details { border-top: 1px dotted #aaa; margin-top: 15px; padding-top: 0; }
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+ .method_details.first { border: 0; }
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+ p.signature, h3.signature {
138
+ font-size: 1.1em; font-weight: normal; font-family: Monaco, Consolas, Courier, monospace;
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+ padding: 6px 10px; margin-top: 18px;
140
+ background: #e5e8ff; border: 1px solid #d8d8e5; -moz-border-radius: 3px; -webkit-border-radius: 3px;
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+ }
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+ p.signature tt,
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+ h3.signature tt { font-family: Monaco, Consolas, Courier, monospace; }
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+ p.signature .overload,
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+ h3.signature .overload { display: block; }
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+ p.signature .extras,
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+ h3.signature .extras { font-weight: normal; font-family: sans-serif; color: #444; font-size: 1em; }
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+ p.signature .not_defined_here,
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+ h3.signature .not_defined_here,
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+ p.signature .aliases,
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+ h3.signature .aliases { display: block; font-weight: normal; font-size: 0.9em; font-family: sans-serif; margin-top: 0px; color: #555; }
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+ p.signature .aliases .names,
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+ h3.signature .aliases .names { font-family: Monaco, Consolas, Courier, monospace; font-weight: bold; color: #000; font-size: 1.2em; }
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+
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+ .tags .tag_title { font-size: 1em; margin-bottom: 0; font-weight: bold; }
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+ .tags ul { margin-top: 5px; padding-left: 30px; list-style: square; }
157
+ .tags ul li { margin-bottom: 3px; }
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+ .tags ul .name { font-family: monospace; font-weight: bold; }
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+ .tags ul .note { padding: 3px 6px; }
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+ .tags { margin-bottom: 12px; }
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+
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+ .tags .examples .tag_title { margin-bottom: 10px; font-weight: bold; }
163
+ .tags .examples .inline p { padding: 0; margin: 0; margin-left: 15px; font-weight: bold; font-size: 0.9em; }
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+
165
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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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+ File: README
8
+
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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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+ </head>
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+ <body>
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+ <div id="header">
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+ <div id="menu">
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+ <a href="_index.html">Index</a> &raquo;
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+ <span class="title">File: README</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"><div id='filecontents'>
65
+ <h1 id="label-parse_fasta">parse_fasta</h1>
66
+
67
+ <p>So you want to parse a fasta file…</p>
68
+
69
+ <h2 id="label-Installation">Installation</h2>
70
+
71
+ <p>Add this line to your application&#39;s Gemfile:</p>
72
+
73
+ <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_gem'>gem</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>&#39;</span></span></code></pre>
74
+
75
+ <p>And then execute:</p>
76
+
77
+ <pre class="code ruby"><code class="ruby">$ bundle</code></pre>
78
+
79
+ <p>Or install it yourself as:</p>
80
+
81
+ <pre class="code ruby"><code class="ruby">$ gem install parse_fasta</code></pre>
82
+
83
+ <h2 id="label-Overview">Overview</h2>
84
+
85
+ <p>Provides the method <code>#each_record</code> for the <code>File</code>
86
+ class.</p>
87
+
88
+ <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_each_record'>each_record</span> <span class='lbrace'>{</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> <span class='id identifier rubyid_block'>block</span> <span class='rbrace'>}</span>
89
+ </code></pre>
90
+
91
+ <p>The whole file is not loaded into memory, so have no fear of giant fasta
92
+ files!</p>
93
+
94
+ <h2 id="label-Usage">Usage</h2>
95
+
96
+ <h3 id="label-Version+1.0.0+%28current%29">Version 1.0.0 (current)</h3>
97
+
98
+ <p>The monkey patch of the <code>File</code> class is no more! Here is the new
99
+ print length example:</p>
100
+
101
+ <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_require'>require</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>&#39;</span></span>
102
+
103
+ <span class='const'>FastaFile</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='const'>ARGV</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</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>
104
+ <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_length'>length</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>
105
+ <span class='kw'>end</span>
106
+ </code></pre>
107
+
108
+ <p>And here, a script to calculate GC content:</p>
109
+
110
+ <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_require'>require</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>&#39;</span></span>
111
+
112
+ <span class='const'>FastaFile</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='const'>ARGV</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</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>
113
+ <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>
114
+ <span class='kw'>end</span>
115
+ </code></pre>
116
+
117
+ <h3 id="label-Version+0.0.5+%28old%29">Version 0.0.5 (old)</h3>
118
+
119
+ <p>An example that lists the length for each sequence. (Won&#39;t work in
120
+ version 1.0.0)</p>
121
+
122
+ <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_require'>require</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>&#39;</span></span>
123
+
124
+ <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='const'>ARGV</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</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>
125
+ <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_length'>length</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>
126
+ <span class='kw'>end</span>
127
+ </code></pre>
128
+
129
+ <h2 id="label-Benchmark">Benchmark</h2>
130
+
131
+ <p>Just for fun, I wanted to compare the execution time to that of BioRuby. I
132
+ calculated sequence length for each fasta record with both the
133
+ <code>each_record</code> method from this gem and using the
134
+ <code>FastaFormat</code> class from BioRuby. You can see the test script in
135
+ <code>benchmark.rb</code>.</p>
136
+
137
+ <p>The test file contained 2,009,897 illumina reads and the file size was 1.1
138
+ gigabytes. Here are the results from Ruby&#39;s <code>Benchmark</code>
139
+ class:</p>
140
+
141
+ <pre class="code ruby"><code class="ruby"> user system total real
142
+ parse_fasta 64.530000 1.740000 66.270000 ( 67.081502)
143
+ bioruby 116.250000 2.260000 118.510000 (120.223710)</code></pre>
144
+
145
+ <p>I just wanted a nice, clean way to parse fasta files, but being nearly
146
+ twice as fasta as BioRuby doesn&#39;t hurt either!</p>
147
+
148
+ <h2 id="label-Notes">Notes</h2>
149
+
150
+ <p>Currently in doesn&#39;t check whether your file is actually a fasta file
151
+ or anything, so watch out.</p>
152
+ </div></div>
153
+
154
+ <div id="footer">
155
+ Generated on Tue Jun 3 22:55:41 2014 by
156
+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
157
+ 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>