fstrozzi-Gmap 1.0.0

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Files changed (32) hide show
  1. data/README +41 -0
  2. data/doc/classes/Gmap.html +129 -0
  3. data/doc/classes/Gmap/Core.html +252 -0
  4. data/doc/classes/Gmap/Core.src/M000006.html +18 -0
  5. data/doc/classes/Gmap/Core.src/M000007.html +25 -0
  6. data/doc/classes/Gmap/Core.src/M000008.html +18 -0
  7. data/doc/classes/Gmap/Core.src/M000009.html +52 -0
  8. data/doc/classes/Gmap/Result.html +337 -0
  9. data/doc/classes/Gmap/Result.src/M000010.html +18 -0
  10. data/doc/classes/Gmap/Result.src/M000011.html +41 -0
  11. data/doc/classes/Gmap/Result.src/M000012.html +22 -0
  12. data/doc/classes/Gmap/Result.src/M000013.html +22 -0
  13. data/doc/classes/Gmap/Result.src/M000014.html +18 -0
  14. data/doc/classes/GmapTest.html +197 -0
  15. data/doc/classes/GmapTest.src/M000001.html +18 -0
  16. data/doc/classes/GmapTest.src/M000002.html +21 -0
  17. data/doc/classes/GmapTest.src/M000003.html +25 -0
  18. data/doc/classes/GmapTest.src/M000004.html +62 -0
  19. data/doc/classes/GmapTest.src/M000005.html +65 -0
  20. data/doc/created.rid +1 -0
  21. data/doc/files/lib/gmap/core_rb.html +118 -0
  22. data/doc/files/lib/gmap_rb.html +101 -0
  23. data/doc/files/test/unit/gmap_test_rb.html +109 -0
  24. data/doc/fr_class_index.html +30 -0
  25. data/doc/fr_file_index.html +29 -0
  26. data/doc/fr_method_index.html +40 -0
  27. data/doc/index.html +24 -0
  28. data/lib/gmap.rb +1 -0
  29. data/lib/gmap/core.rb +269 -0
  30. data/samples/test.gmap +148 -0
  31. data/test/unit/gmap_test.rb +127 -0
  32. metadata +93 -0
data/README ADDED
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+
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+
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+ Author: Francesco Strozzi
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+ Copyright: 2008 Francesco Strozzi
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+ License: The Ruby License
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+
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+ This module allows the parsing of the standard output of Gmap (http://www.gene.com/share/gmap/)
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+
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+ Example:
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+
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+ Gmap::Core.open("output.gmap") do |gmap|
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+
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+ gmap.each_sequence do |seq|
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+
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+ seq.each do |result|
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+
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+ result.query (Query sequence name)
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+ result.target (Target sequence name)
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+ result.q_start (Start coordinate of the query sequence)
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+ result.q_end (End coordinate of the query sequence)
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+ result.start (Start coordintate of the target sequence)
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+ result.end (End coordinate of the target sequence)
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+ result.strand (Strand of the target sequence)
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+ result.exons (# exons found)
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+ result.coverage (Coverage of the query sequence)
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+ result.perc_identity (Pecentage of identity from the alignment)
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+ result.indels (# insertion or deletions)
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+ result.mismatch (# mismatch)
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+ result.aa_change (Prediction of AA changes from mismatches and indels found)
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+ result.aln (Raw alignment between target and query sequences)
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+
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+ ONLY IF GENE MAPS ARE USED WITH GMAP
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+
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+ result.gene_start (Start coordinate of the overlapping gene)
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+ result.gene_end (End coordinate of the overlapping gene)
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+ result.gene_id (ID of the overlapping gene)
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+ end
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+
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+ end
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+
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+ end
data/doc/classes/Gmap.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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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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+ <title>Module: Gmap</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Module</strong></td>
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+ <td class="class-name-in-header">Gmap</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../files/lib/gmap/core_rb.html">
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+ lib/gmap/core.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <table>
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+ <tr><td valign="top">Author:</td><td>Francesco Strozzi
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+
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+ </td></tr>
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+ <tr><td valign="top">Email:</td><td>francesco.strozzi@gmail.com
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+
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+ </td></tr>
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+ <tr><td valign="top">Copyright:</td><td>2008 Francesco Strozzi
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+
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+ </td></tr>
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+ <tr><td valign="top">License:</td><td>The Ruby License
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+
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+ </td></tr>
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+ </table>
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+
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+ </div>
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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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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+ <div id="class-list">
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+ <h3 class="section-bar">Classes and Modules</h3>
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+
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+ Class <a href="Gmap/Core.html" class="link">Gmap::Core</a><br />
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+ Class <a href="Gmap/Result.html" class="link">Gmap::Result</a><br />
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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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+ <!-- if method_list -->
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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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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/classes/Gmap/Core.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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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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+ <title>Class: Gmap::Core</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Class</strong></td>
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+ <td class="class-name-in-header">Gmap::Core</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../files/lib/gmap/core_rb.html">
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+ lib/gmap/core.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ <tr class="top-aligned-row">
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+ <td><strong>Parent:</strong></td>
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+ <td>
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+ Object
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <p>
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+ This module allows the parsing of the standard output of <a
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+ href="../Gmap.html">Gmap</a> (<a
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+ href="http://www.gene.com/share/gmap">www.gene.com/share/gmap</a>/)
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+ </p>
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+ <p>
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+ Example:
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+ </p>
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+ <pre>
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+ Gmap::Core.open(&quot;output.gmap&quot;) do |gmap|
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+
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+ gmap.each_sequence do |seq|
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+
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+ seq.each do |result|
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+
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+ result.query (Query sequence name)
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+ result.target (Target sequence name)
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+ result.q_start (Start coordinate of the query sequence)
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+ result.q_end (End coordinate of the query sequence)
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+ result.start (Start coordintate of the target sequence)
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+ result.end (End coordinate of the target sequence)
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+ result.strand (Strand of the target sequence)
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+ result.exons (# exons found)
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+ result.coverage (Coverage of the query sequence)
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+ result.perc_identity (Pecentage of identity from the alignment)
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+ result.indels (# insertion or deletions)
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+ result.mismatch (# mismatch)
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+ result.aa_change (Prediction of AA changes from mismatches and indels found)
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+ result.aln (Raw alignment between target and query sequences)
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+
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+ ONLY IF GENE MAPS ARE USED WITH GMAP
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+
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+ result.gene_start (Start coordinate of the overlapping gene)
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+ result.gene_end (End coordinate of the overlapping gene)
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+ result.gene_id (ID of the overlapping gene)
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+ end
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+
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+ end
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+
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+ end
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+ </pre>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000008">close</a>&nbsp;&nbsp;
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+ <a href="#M000009">each_sequence</a>&nbsp;&nbsp;
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+ <a href="#M000006">new</a>&nbsp;&nbsp;
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+ <a href="#M000007">open</a>&nbsp;&nbsp;
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+ </div>
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+ </div>
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+
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+
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+
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+ <div id="attribute-list">
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+ <h3 class="section-bar">Attributes</h3>
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+
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+ <div class="name-list">
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+ <table>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">io</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ </table>
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+ </div>
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+ </div>
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+
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+
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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Class methods</h3>
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+
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+ <div id="method-M000006" class="method-detail">
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+ <a name="M000006"></a>
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+
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+ <div class="method-heading">
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+ <a href="Core.src/M000006.html" target="Code" class="method-signature"
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+ onclick="popupCode('Core.src/M000006.html');return false;">
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+ <span class="method-name">new</span><span class="method-args">(io)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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+ </div>
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+
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+ <div id="method-M000007" class="method-detail">
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+ <a name="M000007"></a>
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+
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+ <div class="method-heading">
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+ <a href="Core.src/M000007.html" target="Code" class="method-signature"
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+ onclick="popupCode('Core.src/M000007.html');return false;">
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+ <span class="method-name">open</span><span class="method-args">(file) {|Gmap::Core.new(f)| ...}</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ Open the gmap file for reading
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+ </p>
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+ </div>
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+ </div>
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+
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+ <h3 class="section-bar">Public Instance methods</h3>
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+
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+ <div id="method-M000008" class="method-detail">
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+ <a name="M000008"></a>
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+
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+ <div class="method-heading">
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+ <a href="Core.src/M000008.html" target="Code" class="method-signature"
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+ onclick="popupCode('Core.src/M000008.html');return false;">
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+ <span class="method-name">close</span><span class="method-args">()</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ Close the IO stream on the <a href="../Gmap.html">Gmap</a> file
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+ </p>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000009" class="method-detail">
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+ <a name="M000009"></a>
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+
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+ <div class="method-heading">
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+ <a href="Core.src/M000009.html" target="Code" class="method-signature"
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+ onclick="popupCode('Core.src/M000009.html');return false;">
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+ <span class="method-name">each_sequence</span><span class="method-args">() {|all_results| ...}</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ Iterates on every sequence processed by <a href="../Gmap.html">Gmap</a> and
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+ returns an array of <a href="Result.html">Gmap::Result</a> objects each of
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+ them corresponding to a Path (result) for that sequence
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+ </p>
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+ </div>
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+ </div>
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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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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/classes/Gmap/Core.src/M000006.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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+ <html>
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+ <head>
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+ <title>new (Gmap::Core)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/gmap/core.rb, line 51</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">io</span>)
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+ <span class="ruby-ivar">@io</span> = <span class="ruby-identifier">io</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Gmap/Core.src/M000007.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ 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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+
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+ <html>
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+ <head>
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+ <title>open (Gmap::Core)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/gmap/core.rb, line 57</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">file</span>)
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+
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+ <span class="ruby-identifier">f</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">file</span>)
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block_given?</span>
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+ <span class="ruby-keyword kw">yield</span> <span class="ruby-constant">Gmap</span><span class="ruby-operator">::</span><span class="ruby-constant">Core</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">f</span>)
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+ <span class="ruby-identifier">f</span>.<span class="ruby-identifier">close</span>
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+ <span class="ruby-keyword kw">else</span>
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+ <span class="ruby-constant">Gmap</span><span class="ruby-operator">::</span><span class="ruby-constant">Core</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">f</span>)
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>