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README.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<html xmlns="http://www.w3.org/1999/xhtml">
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<title>The Readme — PyCogent 1.9 documentation</title>
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<div class="headertitle"><a
href="index.html">PyCogent 1.9 documentation</a></div>
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<div class="section" id="the-readme">
<h1>The Readme<a class="headerlink" href="#the-readme" title="Permalink to this headline">¶</a></h1>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Download:</th><td class="field-body"><a class="reference external" href="https://github.com/pycogent/pycogent">From github</a> or follow the <a class="reference internal" href="install.html#quick-install"><span class="std std-ref">Quick installation using pip</span></a> instructions.</td>
</tr>
</tbody>
</table>
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
<p>The toolkit requires Python 2.5.1 or greater, and Numpy 1.3 or greater. Aside from these the dependencies below are optional and the code will work as is. A C compiler, however, will allow external C module’s responsible for the likelihood and matrix exponentiation calculations to be compiled, resulting in significantly improved performance.</p>
<div class="section" id="required">
<span id="id1"></span><h3>Required<a class="headerlink" href="#required" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><a class="reference external" href="http://www.python.org">Python</a>: the language the toolkit is primarily written in, and in which the user writes control scripts.</li>
<li><a class="reference external" href="http://numpy.scipy.org/">Numpy</a>: This is a python module used for speeding up matrix computations. It is available as source code for *nix.</li>
<li><a class="reference external" href="http://www.zlib.net/">zlib</a>: This is a compression library which is available for all platforms and comes pre-installed on most too. If, by chance, your platform doesn’t have this installed then download the source from the <a class="reference external" href="http://www.zlib.net/">zlib</a> site and follow the install instructions, or refer to the instructions for <a class="reference external" href="http://sourceforge.net/projects/pycogent/forums/forum/651121/topic/5635916">compiling matplotlib</a>.</li>
</ul>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">On some linux platforms (like Ubuntu), you must specifically install a <code class="docutils literal"><span class="pre">python-dev</span></code> package so that the <a class="reference external" href="http://www.python.org">Python</a> header files required for building some external dependencies are available.</p>
</div>
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<div class="section" id="optional">
<h3>Optional<a class="headerlink" href="#optional" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li>C compiler: This is standard on most *nix platforms. On Macos X this is available for free in the Developer tools which, if you don’t already have them, can be obtained from <a class="reference external" href="http://www.apple.com">Apple</a>.</li>
<li><a class="reference external" href="http://matplotlib.sourceforge.net">Matplotlib</a>: used to plot several kinds of graphs related to codon usage. For installation, see these instructions for <a class="reference external" href="http://sourceforge.net/projects/pycogent/forums/forum/651121/topic/5635916">compiling matplotlib</a>.</li>
<li><a class="reference external" href="http://www.cython.org/">Cython</a>: This module is only necessary if you are a developer who wants to modify the *.pyx files.</li>
<li><a class="reference external" href="http://code.google.com/p/mpi4py">mpi4py</a>: Message Passing Interface interface, required for parallel computation.</li>
<li><a class="reference external" href="http://www.sqlalchemy.org">SQLAlchemy</a> and a mysql connector such as <a class="reference external" href="https://github.com/PyMySQL/PyMySQL">PyMySQL</a>: These are required for the Ensembl querying code.</li>
</ul>
<p>See the <a class="reference internal" href="install.html#quick-install"><span class="std std-ref">Quick installation using pip</span></a> approach for how these can be grabbed using the <code class="docutils literal"><span class="pre">all</span></code> option..</p>
</div>
</div>
<div class="section" id="installation">
<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h2>
<p>See the <a class="reference internal" href="install.html#quick-install"><span class="std std-ref">Quick installation using pip</span></a>.</p>
</div>
<div class="section" id="testing">
<h2>Testing<a class="headerlink" href="#testing" title="Permalink to this headline">¶</a></h2>
<p><code class="docutils literal"><span class="pre">PyCogent/tests</span></code> contains all the tests. You can most readily run the tests using the <code class="docutils literal"><span class="pre">PyCogent/run_tests</span></code> shell script. This is done by typing:</p>
<div class="highlight-guess"><div class="highlight"><pre><span></span>$ sh run_tests
</pre></div>
</div>
<p>which will automatically build extensions in place, set up the PYTHONPATH and run <code class="docutils literal"><span class="pre">PyCogent/tests/alltests.py</span></code>. Note that if certain optional applications are not installed this will be indicated in the output as “can’t find” or “not installed”. A “<cite>.</cite>” will be printed to screen for each test and if they all pass, you’ll see output like:</p>
<div class="highlight-guess"><div class="highlight"><pre><span></span>Ran 3299 tests in 58.128s
OK
</pre></div>
</div>
</div>
<div class="section" id="tips-for-usage">
<h2>Tips for usage<a class="headerlink" href="#tips-for-usage" title="Permalink to this headline">¶</a></h2>
<p>A good IDE can greatly simplify writing control scripts. Features such as code completion and definition look-up are extremely useful. For a complete list of <a class="reference external" href="http://www.python.org/cgi-bin/moinmoin/PythonEditors">editors go here</a>.</p>
<p>To get help on attributes of an object in python, use</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="nb">dir</span><span class="p">(</span><span class="n">myalign</span><span class="p">)</span>
</pre></div>
</div>
<p>to list the attributes of <code class="docutils literal"><span class="pre">myalign</span></code> or</p>
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">help</span><span class="p">(</span><span class="n">myalign</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">)</span>
</pre></div>
</div>
<p>to figure out how to use the <code class="docutils literal"><span class="pre">myalign.writeToFile</span></code> method. Also note that the directory structure of the package is similar to the import statements required to use a module – to see the contents of <code class="docutils literal"><span class="pre">alignment.py</span></code> or <code class="docutils literal"><span class="pre">sequence.py</span></code> you need to look in the directory <code class="docutils literal"><span class="pre">cogent/core</span></code> path, to use the classes in those files you specify <code class="docutils literal"><span class="pre">cogent.core</span></code> for importing.</p>
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<h3>Table Of Contents</h3>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="install.html">Quick installation using pip</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">The Readme</a></li>
<li class="toctree-l1"><a class="reference internal" href="coding_guidelines.html">Coding guidelines</a></li>
<li class="toctree-l1"><a class="reference internal" href="data_file_links.html">The data files used in the documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="examples/index.html">Cogent Usage Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="cookbook/index.html">PyCogent Cookbook</a></li>
<li class="toctree-l1"><a class="reference internal" href="developer_notes.html">For Developers</a></li>
<li class="toctree-l1"><a class="reference internal" href="scripting_guidelines.html">Scripting guidelines</a></li>
<li class="toctree-l1"><a class="reference internal" href="licenses.html">Licenses and disclaimer</a></li>
<li class="toctree-l1"><a class="reference internal" href="ChangeLog.html">Changelog</a></li>
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