ngs_server 0.1 → 0.2

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data/ext/vcftools/website/src/.svn/text-base/docs.inc.svn-base

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+
+<div class="item">
+
+<h3>Documentation</h3>
+<p>
+The VCFtools package is broadly split into two sections: <br>
+<ul class="faq">
+<li> The <span class="cmd">vcftools</span> binary program, generally used to analyse VCF files.
+<li> The <span class="cmd">Vcf.pm</span> perl module, which is a general Perl API containing a core of
+the utilities <span class="cmd">vcf-convert</span>, <span class="cmd">vcf-merge</span>, 
+<span class="cmd">vcf-compare</span>, <span class="cmd">vcf-isec</span>, and others.
+</ui>
+</p>
+
+<h3>Documentation</h3>
+<ul class="faq">
+<li> <a href="options.html">Documentation for the binary executable <span class="cmd">vcftools</span></a>
+<li> <a href="perl_module.html">The Perl API and scripts</a>
+<li> <a href="#one-liners">Useful shell one-liners</a>
+</ul>
+
+<h3>Examples of usage by topic</h3>
+<ul class="faq">
+<li> <a href="#install">Installation</a>
+<li> <a href="#annotate">Annotating</a>
+<li> <a href="#compare">Comparing</a>
+<li> <a href="#concat">Concatenating</a>
+<li> <a href="#convert">Converting</a>
+<li> <a href="#isec">Intersections, complements</a>
+<li> <a href="#merge">Merging</a>
+<li> <a href="#query">Querying</a>
+<li> <a href="#shuffle">Reordering columns</a>
+<li> <a href="#stats">Stats</a>
+<li> <a href="#subset">Stripping columns</a>
+<li> <a href="#one-liners">Useful shell one-liners</a>
+<li> <a href="#validator">Validating</a>
+<li> <a href="#more">...and more</a>
+</ul>
+</div>
+
+
+<div class="item">
+<a name="install" class="Q">Installation</a>
+<p> The VCFtools package can be decompressed by the command
+<p class="codebox">tar -xzf vcftools_<i>version_number</i>_source.tar.gz</p>
+<p> To build the <span class="cmd">vcftools</span> executable, type "make" in the vcftools folder. </p>
+<p>
+The <b>Perl scripts require that VCF files are compressed by <span class="cmd">bgzip</span>
+and indexed by <span class="cmd">tabix</span></b> (both tools are part of the tabix package, 
+available for <a href="https://sourceforge.net/projects/samtools/files/tabix/">download here</a>).
+Test the tools can be tested by running the script
+<p class="codebox">/path/to/your/installation/perl/test.t</p> 
+For running the Perl scripts, the <b>PERL5LIB environment variable must be set</b> to include the Vcf.pm
+module</p>
+<p class="codebox">export PERL5LIB=/path/to/your/installation/perl</p>
+</div>
+
+
+<div class="item">
+<a name="annotate" class="Q">Annotating</a>
+<p></p>
+<p class="codebox">
+# Add custom annotations <br>
+cat in.vcf | vcf-annotate -a annotations.gz \ <br>
+&nbsp;&nbsp; -d key=INFO,ID=ANN,Number=1,Type=Integer,Description='My custom annotation' \ <br>
+&nbsp;&nbsp; -c CHROM,FROM,TO,INFO/ANN &gt; out.vcf <br>
+<br>
+# Apply SnpCluster filter <br>
+cat in.vcf | <a href="perl_module.html#vcf-annotate">vcf-annotate</a> --filter SnpCluster=3,10 &gt; out.vcf <br>
+</p>
+</div>
+
+
+
+<div class="item">
+<a name="compare" class="Q">Comparing</a>
+<p></p>
+<p class="codebox"><a href="perl_module.html#vcf-compare">vcf-compare</a> A.vcf.gz B.vcf.gz C.vcf.gz
+</p>
+</div>
+
+
+<div class="item">
+<a name="concat" class="Q">Concatenating</a>
+<p></p>
+<p class="codebox"><a href="perl_module.html#vcf-concat">vcf-concat</a> A.vcf.gz B.vcf.gz C.vcf.gz | bgzip -c > out.vcf.gz
+</p>
+</div>
+
+
+<div class="item">
+<a name="convert" class="Q">Converting</a>
+<p></p>
+<p class="codebox">
+# Convert between VCF versions  <br>
+zcat file.vcf.gz | <a href="perl_module.html#vcf-convert">vcf-convert</a> -r reference.fa | bgzip -c &gt; out.vcf.gz  <br>
+<br>
+# Convert from VCF format to tab-delimited text file <br>
+zcat file.vcf.gz | <a href="perl_module.html#vcf-to-tab">vcf-to-tab</a> &gt; out.tab <br>
+</p>
+</div>
+
+
+<div class="item">
+<a name="isec" class="Q">Intersections, complements</a>
+<p></p>
+<p class="codebox">
+# Include positions which appear in at least two files  <br>
+<a href="perl_module.html#vcf-isec">vcf-isec</a> -o -n +2 A.vcf.gz B.vcf.gz C.vcf.gz | bgzip -c &gt; out.vcf.gz <br>
+<br>
+# Exclude from A positions which appear in B and/or C   <br>
+<a href="perl_module.html#vcf-isec">vcf-isec</a> -c A.vcf.gz B.vcf.gz C.vcf.gz | bgzip -c &gt; out.vcf.gz   <br>
+</p>
+</div>
+
+
+<div class="item">
+<a name="merge" class="Q">Merging</a>
+<p></p>
+<p class="codebox">
+<a href="perl_module.html#vcf-merge">vcf-merge</a> A.vcf.gz B.vcf.gz | bgzip -c &gt; C.vcf.gz
+</p>
+</div>
+
+<div class="item">
+<a name="isec" class="Q">Querying</a>
+<p></p>
+<p class="codebox"><a href="perl_module.html#vcf-query">vcf-query</a> file.vcf.gz 1:10327-10330 -c NA0001
+</p>
+</div>
+
+
+
+<div class="item">
+<a name="shuffle" class="Q">Reordering columns</a>
+<p></p>
+<p class="codebox"><a href="perl_module.html#vcf-shuffle-cols">vcf-shuffle-cols</a> -t template.vcf.gz file.vcf.gz > out.vcf
+</p>
+</div>
+
+
+<div class="item">
+<a name="stats" class="Q">Stats</a>
+<p></p>
+<p class="codebox"><a href="perl_module.html#vcf-stats">vcf-stats</a> file.vcf.gz
+</p>
+</div>
+
+
+<div class="item">
+<a name="subset" class="Q">Stripping columns</a>
+<p></p>
+<p class="codebox"><a href="perl_module.html#vcf-subset">vcf-subset</a> -c NA0001,NA0002 file.vcf.gz | bgzip -c &gt; out.vcf.gz
+</p>
+</div>
+
+
+
+<div class="item">
+<a name="one-liners" class="Q">Useful shell one-liners</a>
+<p> This sections lists some usefull one line commands. Note that there are also dedicated convenience scripts
+<a href="perl_module.html#vcf-sort">vcf-sort</a> and <a href="perl_module.html#vcf-concat">vcf-concat</a> 
+which do the same but also perform some basic sanity checks.
+All examples in BASH.</p>
+<p class="codebox">
+# Replace VCF header. The file must be compressed by bgzip. <br>
+tabix -r header.txt in.vcf.gz > out.vcf.gz                  <br>
+<br>
+# Sort VCF file keeping the header. The head command is for performance.    <br>
+(zcat file.vcf.gz | head -100 | grep ^#;                                    <br>
+ zcat file.vcf.gz | grep -v ^# | sort -k1,1d -k2,2n;)  \                    <br>
+ | bgzip -c &gt; out.vcf.gz <br>
+<br>
+# Merge (that is, concatenate) two VCF files into one, keeping the header   <br>
+#   from first one only.                    <br>
+(zcat A.vcf.gz | head -100 | grep ^#; \     <br>
+ zcat A.vcf.gz | grep -v ^#;          \     <br>
+ zcat B.vcf.gz | grep -v ^#; )        \     <br>
+ | bgzip -c &gt; out.vcf.gz     
+</p>
+</div>
+
+
+<div class="item">
+<a name="validator" class="Q">VCF validation</a>
+<p> Both <span class="cmd">vcftools</span> and <span class="cmd">Vcf.pm</span> can be used for validation. The
+    first validates VCFv4.0, the latter is able to validate the older versions as well.
+</p>
+<p class="codebox">
+perl -M<a href="perl_module.html#Vcf.pm">Vcf</a> -e validate example.vcf  <br>
+perl -I/path/to/the/module/ -M<a href="perl_module.html#Vcf.pm">Vcf</a> -e validate example.vcf   <br>
+<a href="perl_module.html#vcf-validator">vcf-validator</a> example.vcf
+</p>
+</div>
+
+
+<div class="item">
+<a name="more" class="Q">...and more</a>
+<p>This page gives just a list of basic capabilities. For more, please go to the <a href="options.html">vcftools's options</a> page
+and the <a href="perl_module.html">Perl API and scripts</a> page.</p>
+</div>
+

data/ext/vcftools/website/src/.svn/text-base/index.inc.svn-base

@@ -0,0 +1,52 @@
+
+<div class="item">
+    <h1>Welcome to VCFtools</h1>
+    <p>Welcome to VCFtools - a program package designed for working with VCF
+    files, such as those generated by the 1000 Genomes Project. The aim of
+    VCFtools is to provide methods for working with VCF files: validating, 
+    merging, comparing and calculate some basic population genetic statistics.
+    </p>
+</div>
+
+<div class="item">
+    <h3>Supported VCF versions</h3>
+    <p>VCFtools supports the <a href="specs.html">VCF format v4.0</a>. The 
+    vcf-validator, Perl API and scripts now support also <a href="specs.html">VCF format v4.1</a> and 
+    maintain backward compatibility with older versions.
+    <br>
+    For details, please go to the <a href="docs.html">Documentation</a> page.</p>
+</div>
+
+<div class="item">
+    <h3>Mailing List</h3>
+    <p>Anything VCF or VCFtools related may be discussed on the project's <a href="http://sourceforge.net/mail/?group_id=279407">mailing list</a>.</p>
+</div>
+
+<div class="item">
+    <h3>Download</h3>
+    <p>
+    The <b>latest stable release</b> can be downloaded from here:</p>
+    <p class="codebox" style="text-align: center;"><a href="https://sourceforge.net/projects/vcftools/files/">https://sourceforge.net/projects/vcftools/files/</a></p>
+    <p>
+    The <b>latest development version</b> can be retrieved by running the following command:
+    </p>
+    <p class="codebox" style="text-align: center;"> svn checkout https://vcftools.svn.sourceforge.net/svnroot/vcftools vcftools </p>
+    <p>
+    The above command is required to be run only once, for any subsequent updates run this command from the vcftools directory: 
+    </p>
+    <p class="codebox" style="text-align: center;"> svn update </p>
+    </div>
+    <div class="item">
+    <h3>How to use</h3>
+    The VCFtools package includes a set of tools for
+    <ul>
+    <li> validating
+    <li> comparing
+    <li> merging 
+    <li> annotating
+    <li> creating intersections and subsets
+    <li> ...
+    </ul>
+    For details, please go to the <a href="docs.html">Documentation</a> page.
+</div>
+

data/ext/vcftools/website/src/.svn/text-base/index.php.svn-base

@@ -0,0 +1,80 @@
+<?php
+
+function validate_path($path)
+{
+    if ( preg_match("/^[A-Za-z0-9_]+$/",$path) && file_exists("src/$path.inc") ) return $path;
+    return "index";
+}
+
+$titles = array(
+        'index'         => 'VCFtools',
+        'perl_module'   => 'VCFtools: Perl tools and API',
+        'docs'          => 'VCFtools Documentation',
+        'license'       => 'VCFtools License',
+        'specs'         => 'VCF Specification',
+        'links'         => 'VCF Links',
+        'options'       => 'vcftools Options',
+        );
+
+if (isset($argc)) { $_GET['pg']=$argv[1]; }
+$path  = array_key_exists('pg',$_GET) ? validate_path($_GET['pg']) : 'index';
+$title = array_key_exists($path,$titles) ? $titles[$path] : $titles['index'];
+
+
+?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
+<html>
+<head>
+    <script type="text/javascript">
+        var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+        document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+    </script>
+    <script type="text/javascript">
+        try {
+            var pageTracker = _gat._getTracker("UA-272183-4");
+            pageTracker._trackPageview();
+        } catch(err) {}
+    </script>
+
+    <meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
+    <link rel="stylesheet" type="text/css" href="default.css" media="screen">
+    <link href='favicon.png' rel='shortcut icon' type='image/png'>
+    <link href='favicon.png' rel='icon' type='image/png'>
+    
+    <title><?php echo $title; ?></title>
+</head>
+
+
+
+<body>
+<div class="container">
+<div class="main">
+    <div class="header">
+    <div class="title">
+        <a href="index.html">VCFtools</a>
+    </div>
+    </div>
+<div class="content">
+
+<?php 
+    include("$path.inc");
+?>
+
+</div>
+
+<div class="sidenav">
+    <h1>Navigation</h1>
+    <ul>
+    <li><a href="index.html">Main</a></li>
+    <li><a href="http://sourceforge.net/projects/vcftools/">Sourceforge page</a></li>
+    <li><a href="docs.html">Documentation</a></li>
+    <li><a href="license.html">License</a></li>
+    <li><a href="specs.html">VCF specification</a></li>
+    <li><a href="links.html">Links</a></li>
+    <li><a href="http://www.1000genomes.org/">1000 Genomes</a></li>
+    </ul>
+</div>
+<div class="clearer"><span></span></div>
+</div>
+</div>
+</body></html>