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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<title>CNV Analysis — baseq 0.01 documentation</title>
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<div class="section" id="cnv-analysis">
<span id="cnv"></span><h1>CNV Analysis<a class="headerlink" href="#cnv-analysis" title="Permalink to this headline">¶</a></h1>
<p>CNV analysis is for: XXXX</p>
<div class="section" id="config">
<h2>Config<a class="headerlink" href="#config" title="Permalink to this headline">¶</a></h2>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="o">[</span>CNV<span class="o">]</span>
<span class="nv">bowtie2</span> <span class="o">=</span> /mnt/gpfs/Database/softs/anaconda2/bin/bowtie2
<span class="nv">samtools</span> <span class="o">=</span> /mnt/gpfs/Database/softs/anaconda2/bin/samtools
<span class="o">[</span>CNV_ref_hg19<span class="o">]</span>
<span class="nv">bowtie2_index</span> <span class="o">=</span> /mnt/gpfs/Database/ref/hg19/hg19
<span class="nv">dynamic_bin</span> <span class="o">=</span> /mnt/gpfs/Users/zhangxiannian/basematic/cnv/hg19.dynabin.txt
</pre></div>
</div>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>mkdir myproject
<span class="nb">cd</span> myproject
python3 -m venv venv
</pre></div>
</div>
</div>
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
<p>These distributions will be installed automatically when installing Flask.</p>
<ul class="simple">
<li><a class="reference external" href="http://werkzeug.pocoo.org/">Werkzeug</a> implements WSGI, the standard Python interface between
applications and servers.</li>
<li><a class="reference external" href="http://jinja.pocoo.org/">Jinja</a> is a template language that renders the pages your application
serves.</li>
<li><a class="reference external" href="https://pypi.org/project/MarkupSafe/">MarkupSafe</a> comes with Jinja. It escapes untrusted input when rendering
templates to avoid injection attacks.</li>
<li><a class="reference external" href="https://pythonhosted.org/itsdangerous/">ItsDangerous</a> securely signs data to ensure its integrity. This is used
to protect Flask’s session cookie.</li>
<li><a class="reference external" href="http://click.pocoo.org/">Click</a> is a framework for writing command line applications. It provides
the <code class="docutils literal notranslate"><span class="pre">flask</span></code> command and allows adding custom management commands.</li>
</ul>
<div class="section" id="optional-dependencies">
<h3>Optional dependencies<a class="headerlink" href="#optional-dependencies" title="Permalink to this headline">¶</a></h3>
<p>These distributions will not be installed automatically. Flask will detect and
use them if you install them.</p>
<ul class="simple">
<li><a class="reference external" href="https://pythonhosted.org/blinker/">Blinker</a> provides support for <span class="xref std std-ref">signals</span>.</li>
<li><a class="reference external" href="https://simplejson.readthedocs.io/">SimpleJSON</a> is a fast JSON implementation that is compatible with
Python’s <code class="docutils literal notranslate"><span class="pre">json</span></code> module. It is preferred for JSON operations if it is
installed.</li>
<li><a class="reference external" href="https://github.com/theskumar/python-dotenv#readme">python-dotenv</a> enables support for <span class="xref std std-ref">dotenv</span> when running <code class="docutils literal notranslate"><span class="pre">flask</span></code>
commands.</li>
<li><a class="reference external" href="https://pythonhosted.org/watchdog/">Watchdog</a> provides a faster, more efficient reloader for the development
server.</li>
</ul>
</div>
</div>
<div class="section" id="virtual-environments">
<h2>Virtual environments<a class="headerlink" href="#virtual-environments" title="Permalink to this headline">¶</a></h2>
<p>Use a virtual environment to manage the dependencies for your project, both in
development and in production.</p>
<p>What problem does a virtual environment solve? The more Python projects you
have, the more likely it is that you need to work with different versions of
Python libraries, or even Python itself. Newer versions of libraries for one
project can break compatibility in another project.</p>
<p>Virtual environments are independent groups of Python libraries, one for each
project. Packages installed for one project will not affect other projects or
the operating system’s packages.</p>
<p>Python 3 comes bundled with the <code class="xref py py-mod docutils literal notranslate"><span class="pre">venv</span></code> module to create virtual
environments. If you’re using a modern version of Python, you can continue on
to the next section.</p>
<p>If you’re using Python 2, see <a class="reference internal" href="installation.html#install-install-virtualenv"><span class="std std-ref">Install virtualenv</span></a> first.</p>
<div class="section" id="create-an-environment">
<span id="install-create-env"></span><h3>Create an environment<a class="headerlink" href="#create-an-environment" title="Permalink to this headline">¶</a></h3>
<p>Create a project folder and a <code class="file docutils literal notranslate"><span class="pre">venv</span></code> folder within:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>mkdir myproject
<span class="nb">cd</span> myproject
python3 -m venv venv
</pre></div>
</div>
<p>On Windows:</p>
<div class="highlight-bat notranslate"><div class="highlight"><pre><span></span>py -3 -m venv venv
</pre></div>
</div>
<p>If you needed to install virtualenv because you are on an older version of
Python, use the following command instead:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>virtualenv venv
</pre></div>
</div>
<p>On Windows:</p>
<div class="highlight-bat notranslate"><div class="highlight"><pre><span></span>\Python27\Scripts\virtualenv.exe venv
</pre></div>
</div>
</div>
<div class="section" id="activate-the-environment">
<span id="install-activate-env"></span><h3>Activate the environment<a class="headerlink" href="#activate-the-environment" title="Permalink to this headline">¶</a></h3>
<p>Before you work on your project, activate the corresponding environment:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>. venv/bin/activate
</pre></div>
</div>
<p>On Windows:</p>
<div class="highlight-bat notranslate"><div class="highlight"><pre><span></span>venv\Scripts\activate
</pre></div>
</div>
<p>Your shell prompt will change to show the name of the activated environment.</p>
</div>
</div>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">CNV Analysis</a><ul>
<li><a class="reference internal" href="#config">Config</a></li>
<li><a class="reference internal" href="#dependencies">Dependencies</a><ul>
<li><a class="reference internal" href="#optional-dependencies">Optional dependencies</a></li>
</ul>
</li>
<li><a class="reference internal" href="#virtual-environments">Virtual environments</a><ul>
<li><a class="reference internal" href="#create-an-environment">Create an environment</a></li>
<li><a class="reference internal" href="#activate-the-environment">Activate the environment</a></li>
</ul>
</li>
</ul>
</li>
</ul>
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<h3>Related Topics</h3>
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<li><a href="index.html">Documentation overview</a><ul>
<li>Previous: <a href="BAM.html" title="previous chapter">BAM File Manipulation</a></li>
<li>Next: <a href="SNV.html" title="next chapter">SNV Analysis</a></li>
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