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- <h1>Source code for biolite.wrappers</h1><div class="highlight"><pre>
- <span class="c"># BioLite - Tools for processing gene sequence data and automating workflows</span>
- <span class="c"># Copyright (c) 2012-2013 Brown University. All rights reserved.</span>
- <span class="c"># </span>
- <span class="c"># This file is part of BioLite.</span>
- <span class="c"># </span>
- <span class="c"># BioLite is free software: you can redistribute it and/or modify</span>
- <span class="c"># it under the terms of the GNU General Public License as published by</span>
- <span class="c"># the Free Software Foundation, either version 3 of the License, or</span>
- <span class="c"># (at your option) any later version.</span>
- <span class="c"># </span>
- <span class="c"># BioLite is distributed in the hope that it will be useful,</span>
- <span class="c"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
- <span class="c"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
- <span class="c"># GNU General Public License for more details.</span>
- <span class="c"># </span>
- <span class="c"># You should have received a copy of the GNU General Public License</span>
- <span class="c"># along with BioLite. If not, see <http://www.gnu.org/licenses/>.</span>
- <span class="sd">"""</span>
- <span class="sd">A series of wrappers for external calls to various bioinformatics tools.</span>
- <span class="sd">"""</span>
- <span class="kn">import</span> <span class="nn">glob</span>
- <span class="kn">import</span> <span class="nn">os</span>
- <span class="kn">import</span> <span class="nn">random</span>
- <span class="kn">import</span> <span class="nn">shlex</span>
- <span class="kn">import</span> <span class="nn">subprocess</span>
- <span class="kn">import</span> <span class="nn">sys</span>
- <span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">namedtuple</span>
- <span class="kn">import</span> <span class="nn">config</span>
- <span class="kn">import</span> <span class="nn">diagnostics</span>
- <span class="kn">import</span> <span class="nn">utils</span>
- <div class="viewcode-block" id="BaseWrapper"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.BaseWrapper">[docs]</a><span class="k">class</span> <span class="nc">BaseWrapper</span><span class="p">:</span>
- <span class="sd">"""</span>
- <span class="sd"> A base class that handles generic wrapper functionality.</span>
- <span class="sd"> </span>
- <span class="sd"> Wrappers for specific programs should inherit this class, call `self.init`</span>
- <span class="sd"> to specify their `name` (which is a key into the executable entries in the</span>
- <span class="sd"> BioLite configuration file), and append their arguments to the `self.args`</span>
- <span class="sd"> list.</span>
- <span class="sd"> By convention, a wrapper should call `self.run()` as the final line in its</span>
- <span class="sd"> `__init__` function. This allows for clean syntax and use of the wrapper</span>
- <span class="sd"> directly, without assigning it to a variable name, e.g.</span>
- <span class="sd"> wrappers.MyWrapper(arg1, arg2, ...)</span>
- <span class="sd"> When your wrapper runs, BaseWrapper will do the following:</span>
- <span class="sd"> * log the complete command line to diagnostics;</span>
- <span class="sd"> * optionally call the program with a version flag (invoked with `version`)</span>
- <span class="sd"> to obtain a version string, then log this to the :ref:`programs-table`</span>
- <span class="sd"> along with a hash of the binary executable file;</span>
- <span class="sd"> * append the command's stderr to a file called `name`.log in the CWD;</span>
- <span class="sd"> * also append the command's stdout to the same log file, unless you set</span>
- <span class="sd"> `self.stdout`, in which case stdout is redirected to a file of that name;</span>
- <span class="sd"> * on Linux, add a memory profiling library to the LD_PRELOAD environment</span>
- <span class="sd"> variable;</span>
- <span class="sd"> * call the command and check its return code (which should be 0 on success,</span>
- <span class="sd"> unless you specify a different code with `self.return_ok`), optionally</span>
- <span class="sd"> using the CWD specified in `self.cwd` or the environment specified in</span>
- <span class="sd"> `self.env`.</span>
- <span class="sd"> * parse the stderr of the command to find [biolite.profile] markers and</span>
- <span class="sd"> use the rusage values from `utils.safe_call` to populate a profile</span>
- <span class="sd"> entity in the diagnostics with walltime, usertime, systime, mem, and</span>
- <span class="sd"> vmem attributes.</span>
- <span class="sd"> """</span>
-
- <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">cmd</span> <span class="o">=</span> <span class="n">config</span><span class="o">.</span><span class="n">get_command</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">=</span> <span class="p">[]</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">return_ok</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">cwd</span> <span class="o">=</span> <span class="bp">None</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="bp">None</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">env</span> <span class="o">=</span> <span class="bp">None</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">max_concurrency</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">maxint</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">output_patterns</span> <span class="o">=</span> <span class="bp">None</span>
- <span class="n">init</span> <span class="o">=</span> <span class="n">__init__</span>
- <span class="sd">"""A shortcut for calling the BaseWrapper __init__ from a subclass."""</span>
- <div class="viewcode-block" id="BaseWrapper.check_arg"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.BaseWrapper.check_arg">[docs]</a> <span class="k">def</span> <span class="nf">check_arg</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">flag</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> If `value` evaluates to True, append `flag` and `value` to the argument</span>
- <span class="sd"> list.</span>
- <span class="sd"> """</span>
- <span class="k">if</span> <span class="n">value</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">flag</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
- </div>
- <div class="viewcode-block" id="BaseWrapper.add_threading"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.BaseWrapper.add_threading">[docs]</a> <span class="k">def</span> <span class="nf">add_threading</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">flag</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> Indicates that this wrapper should use threading by appending an</span>
- <span class="sd"> argument with the specified `flag` followed by the number of threads</span>
- <span class="sd"> specified in the BioLite configuration file.</span>
- <span class="sd"> """</span>
- <span class="n">threads</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">config</span><span class="o">.</span><span class="n">get_resource</span><span class="p">(</span><span class="s">'threads'</span><span class="p">)),</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_concurrency</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">threads</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">flag</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">threads</span><span class="p">)</span>
- </div>
- <div class="viewcode-block" id="BaseWrapper.add_openmp"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.BaseWrapper.add_openmp">[docs]</a> <span class="k">def</span> <span class="nf">add_openmp</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> Indicates that this wrapper should use OpenMP by setting the</span>
- <span class="sd"> $OMP_NUM_THREADS environment variable equal to the number of threads</span>
- <span class="sd"> specified in the BioLite configuration file.</span>
- <span class="sd"> """</span>
- <span class="n">threads</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">config</span><span class="o">.</span><span class="n">get_resource</span><span class="p">(</span><span class="s">'threads'</span><span class="p">)),</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_concurrency</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">env</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="p">[</span><span class="s">'OMP_NUM_THREADS'</span><span class="p">]</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">threads</span><span class="p">)</span>
- </div>
- <div class="viewcode-block" id="BaseWrapper.version"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.BaseWrapper.version">[docs]</a> <span class="k">def</span> <span class="nf">version</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">flag</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">cmd</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> Generates and logs a hash to distinguish this particular installation</span>
- <span class="sd"> of the program (on a certain host, with a certain compiler, program</span>
- <span class="sd"> version, etc.)</span>
- <span class="sd"> Specify the optional 'binary' argument if the wrapper name is not</span>
- <span class="sd"> actually the program, e.g. if your program has a Perl wrapper script.</span>
- <span class="sd"> Set 'binary' to the binary program that is likely to change between</span>
- <span class="sd"> versions.</span>
- <span class="sd"> Specify the optional 'cmd' argument if the command to run for version</span>
- <span class="sd"> information is different than what will be invoked by `run` (e.g.</span>
- <span class="sd"> if the program has a perl wrapper script, but you want to version an</span>
- <span class="sd"> underlying binary executable).</span>
- <span class="sd"> """</span>
- <span class="c"># Setup the command to run.</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">cmd</span><span class="p">:</span>
- <span class="n">cmd</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cmd</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">flag</span><span class="p">:</span>
- <span class="n">cmd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">flag</span><span class="p">)</span>
- <span class="c"># Run the command.</span>
- <span class="k">try</span><span class="p">:</span>
- <span class="n">vstring</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">check_output</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">stderr</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">STDOUT</span><span class="p">)</span>
- <span class="k">except</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">CalledProcessError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
- <span class="n">vstring</span> <span class="o">=</span> <span class="n">e</span><span class="o">.</span><span class="n">output</span>
- <span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
- <span class="n">utils</span><span class="o">.</span><span class="n">failed_executable</span><span class="p">(</span><span class="n">cmd</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">e</span><span class="p">)</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">path</span><span class="p">:</span>
- <span class="n">path</span> <span class="o">=</span> <span class="n">cmd</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
- <span class="c"># Generate a hash.</span>
- <span class="n">vhash</span> <span class="o">=</span> <span class="n">diagnostics</span><span class="o">.</span><span class="n">log_program_version</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">vstring</span><span class="p">,</span> <span class="n">path</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">vhash</span><span class="p">:</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">prefix</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'version'</span><span class="p">,</span> <span class="n">vhash</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">prefix</span><span class="o">.</span><span class="n">pop</span><span class="p">()</span>
- </div>
- <div class="viewcode-block" id="BaseWrapper.version_jar"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.BaseWrapper.version_jar">[docs]</a> <span class="k">def</span> <span class="nf">version_jar</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> Special case of version() when the executable is a JAR file.</span>
- <span class="sd"> """</span>
- <span class="n">cmd</span> <span class="o">=</span> <span class="n">config</span><span class="o">.</span><span class="n">get_command</span><span class="p">(</span><span class="s">'java'</span><span class="p">)</span>
- <span class="n">cmd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'-jar'</span><span class="p">)</span>
- <span class="n">cmd</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cmd</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="n">cmd</span><span class="o">=</span><span class="n">cmd</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">cmd</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
- </div>
- <div class="viewcode-block" id="BaseWrapper.run"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.BaseWrapper.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cmd</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> Call this function at the end of your class's `__init__` function.</span>
- <span class="sd"> """</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">cmd</span><span class="p">:</span>
- <span class="n">cmd</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cmd</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'command_executable'</span><span class="p">,</span> <span class="s">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
- <span class="n">cmd</span> <span class="o">+=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">prefix</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'command'</span><span class="p">,</span> <span class="s">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'command_list'</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
- <span class="n">stderr_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s">'.log'</span><span class="p">)</span>
- <span class="n">stderr_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">stderr_path</span><span class="p">,</span> <span class="s">'a'</span><span class="p">)</span>
- <span class="k">print</span> <span class="o">>></span> <span class="n">stderr_file</span><span class="p">,</span> <span class="s">"[biolite] timestamp=</span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">utils</span><span class="o">.</span><span class="n">timestamp</span><span class="p">()</span>
- <span class="n">stderr_file</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'log'</span><span class="p">,</span> <span class="n">stderr_path</span><span class="p">)</span>
- <span class="c"># Write to a stdout file if it was set by the derived class.</span>
- <span class="c"># Otherwise, stdout and stderr will be combined into the log file.</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">stdout</span><span class="p">:</span>
- <span class="n">stdout_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'stdout'</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
- <span class="k">else</span><span class="p">:</span>
- <span class="n">stdout_file</span> <span class="o">=</span> <span class="n">stderr_file</span>
- <span class="c"># Setup memory profiling on Linux.</span>
- <span class="k">if</span> <span class="n">config</span><span class="o">.</span><span class="n">kernel</span> <span class="o">==</span> <span class="s">'Linux'</span><span class="p">:</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">env</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
- <span class="n">old_preload</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'LD_PRELOAD'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="p">[</span><span class="s">'LD_PRELOAD'</span><span class="p">]</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">config</span><span class="o">.</span><span class="n">libdir</span><span class="p">,</span> <span class="s">'libmemusage.so'</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">old_preload</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="p">[</span><span class="s">'LD_PRELOAD'</span><span class="p">]</span> <span class="o">+=</span> <span class="s">":</span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">old_preload</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">"LD_PRELOAD"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="p">[</span><span class="s">'LD_PRELOAD'</span><span class="p">])</span>
- <span class="n">retcode</span><span class="p">,</span> <span class="n">walltime</span><span class="p">,</span> <span class="n">rusage</span> <span class="o">=</span> <span class="n">utils</span><span class="o">.</span><span class="n">safe_call</span><span class="p">(</span>
- <span class="n">cmd</span><span class="p">,</span>
- <span class="n">stdout</span><span class="o">=</span><span class="n">stdout_file</span><span class="p">,</span>
- <span class="n">stderr</span><span class="o">=</span><span class="n">stderr_file</span><span class="p">,</span>
- <span class="n">cwd</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">cwd</span><span class="p">,</span>
- <span class="n">return_ok</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">return_ok</span><span class="p">,</span>
- <span class="n">env</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="p">)</span>
- <span class="c"># Log profile.</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">prefix</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'profile'</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'name'</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'return'</span><span class="p">,</span> <span class="n">retcode</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'walltime'</span><span class="p">,</span> <span class="n">walltime</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'usertime'</span><span class="p">,</span> <span class="n">rusage</span><span class="o">.</span><span class="n">ru_utime</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'systime'</span><span class="p">,</span> <span class="n">rusage</span><span class="o">.</span><span class="n">ru_stime</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">config</span><span class="o">.</span><span class="n">kernel</span> <span class="o">==</span> <span class="s">'Darwin'</span><span class="p">:</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">'mem'</span><span class="p">,</span> <span class="n">rusage</span><span class="o">.</span><span class="n">ru_maxrss</span> <span class="o">/</span> <span class="mi">1024</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">prefix</span><span class="o">.</span><span class="n">pop</span><span class="p">()</span>
- <span class="n">stderr_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">stdout</span><span class="p">:</span>
- <span class="n">stdout_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
- <span class="c"># Reverse any output patterns, since they will be matched against</span>
- <span class="c"># program output from the last line backward.</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">output_patterns</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">output_patterns</span><span class="o">.</span><span class="n">reverse</span><span class="p">()</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">log_program_output</span><span class="p">(</span><span class="n">stderr_path</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">output_patterns</span><span class="p">)</span>
- <span class="n">diagnostics</span><span class="o">.</span><span class="n">prefix</span><span class="o">.</span><span class="n">pop</span><span class="p">()</span>
- </div>
- <div class="viewcode-block" id="BaseWrapper.run_jar"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.BaseWrapper.run_jar">[docs]</a> <span class="k">def</span> <span class="nf">run_jar</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mem</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> Special case of run() when the executable is a JAR file.</span>
- <span class="sd"> """</span>
- <span class="n">cmd</span> <span class="o">=</span> <span class="n">config</span><span class="o">.</span><span class="n">get_command</span><span class="p">(</span><span class="s">'java'</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">mem</span><span class="p">:</span>
- <span class="n">cmd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'-Xmx</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="n">mem</span><span class="p">)</span>
- <span class="n">cmd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'-jar'</span><span class="p">)</span>
- <span class="n">cmd</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cmd</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="p">)</span>
- </div></div>
- <div class="viewcode-block" id="estimate_insert_size"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.estimate_insert_size">[docs]</a><span class="k">def</span> <span class="nf">estimate_insert_size</span><span class="p">():</span>
- <span class="sd">"""</span>
- <span class="sd"> For tools that need insert sizes, use available estimates from the</span>
- <span class="sd"> diagnostics database, or resort to the default values in the BioLite</span>
- <span class="sd"> configuration file.</span>
- <span class="sd"> Returns an AttributeDict with the fields `mean`, `stddev` and `max`.</span>
- <span class="sd"> """</span>
- <span class="n">entity</span> <span class="o">=</span> <span class="n">diagnostics</span><span class="o">.</span><span class="n">INSERT_SIZE</span>
- <span class="n">size</span> <span class="o">=</span> <span class="n">utils</span><span class="o">.</span><span class="n">AttributeDict</span><span class="p">()</span>
- <span class="c"># Try the diagnostics cache, if the estimate is from an earlier stage</span>
- <span class="c"># of the current pipeline.</span>
- <span class="n">size</span><span class="o">.</span><span class="n">mean</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">diagnostics</span><span class="o">.</span><span class="n">local_lookup</span><span class="p">(</span><span class="n">entity</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'mean'</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
- <span class="n">size</span><span class="o">.</span><span class="n">stddev</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">diagnostics</span><span class="o">.</span><span class="n">local_lookup</span><span class="p">(</span><span class="n">entity</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'stddev'</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
- <span class="n">size</span><span class="o">.</span><span class="n">max</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">size</span><span class="o">.</span><span class="n">mean</span><span class="p">:</span>
- <span class="c"># Search the global diagnostics database (passing None to lookup_by_id</span>
- <span class="c"># will use the currently initialized id in diagnostics.</span>
- <span class="n">values</span> <span class="o">=</span> <span class="n">diagnostics</span><span class="o">.</span><span class="n">lookup_by_id</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="n">entity</span><span class="p">)</span>
- <span class="n">size</span><span class="o">.</span><span class="n">mean</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">values</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'mean'</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
- <span class="n">size</span><span class="o">.</span><span class="n">stddev</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">values</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'stddev'</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">size</span><span class="o">.</span><span class="n">mean</span><span class="p">:</span>
- <span class="n">size</span><span class="o">.</span><span class="n">mean</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">config</span><span class="o">.</span><span class="n">get_resource</span><span class="p">(</span><span class="s">'max_insert_size'</span><span class="p">))</span>
- <span class="n">size</span><span class="o">.</span><span class="n">stddev</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">config</span><span class="o">.</span><span class="n">get_resource</span><span class="p">(</span><span class="s">'mean_insert_size'</span><span class="p">))</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">size</span><span class="o">.</span><span class="n">max</span><span class="p">:</span>
- <span class="n">size</span><span class="o">.</span><span class="n">max</span> <span class="o">=</span> <span class="n">size</span><span class="o">.</span><span class="n">mean</span> <span class="o">+</span> \
- <span class="n">size</span><span class="o">.</span><span class="n">stddev</span> <span class="o">*</span> <span class="nb">int</span><span class="p">(</span><span class="n">config</span><span class="o">.</span><span class="n">get_resource</span><span class="p">(</span><span class="s">'max_insert_stddev'</span><span class="p">))</span>
- <span class="k">return</span> <span class="n">size</span>
- <span class="c">### BioLite command line tools ###</span>
- </div>
- <div class="viewcode-block" id="CountLines"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.CountLines">[docs]</a><span class="k">class</span> <span class="nc">CountLines</span> <span class="p">(</span><span class="n">BaseWrapper</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> usage: count_lines [-t THREADS] [INPUT ...]</span>
- <span class="sd"> Count the number of lines in the INPUT files using multiple threads to</span>
- <span class="sd"> increase throughput.</span>
- <span class="sd"> """</span>
- <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">inputs</span><span class="p">):</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="s">'count_lines'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="s">'-v'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">add_threading</span><span class="p">(</span><span class="s">'-t'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">+=</span> <span class="n">inputs</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
- </div>
- <div class="viewcode-block" id="Coverage"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.Coverage">[docs]</a><span class="k">class</span> <span class="nc">Coverage</span> <span class="p">(</span><span class="n">BaseWrapper</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> usage: coverage [-i SAM] [-o STATS]</span>
- <span class="sd"> Parses a SAM alignment file and writes a coverage table to STATS with</span>
- <span class="sd"> columns for the reference name, the length of the referene, and the number</span>
- <span class="sd"> of reads covering it in the alignment.</span>
- <span class="sd"> """</span>
- <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sam</span><span class="p">,</span> <span class="n">stats</span><span class="p">):</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="s">'coverage'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="s">'-v'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">+=</span> <span class="p">(</span><span class="s">'-i'</span><span class="p">,</span> <span class="n">sam</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="n">stats</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
- </div>
- <div class="viewcode-block" id="Exclude"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.Exclude">[docs]</a><span class="k">class</span> <span class="nc">Exclude</span> <span class="p">(</span><span class="n">BaseWrapper</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> usage: exclude -x EXCLUDE_FILE [-k] [...] [-i INPUT ...] [-o OUTPUT ...]</span>
- <span class="sd"> Filters all the reads in the input files (FASTA or FASTQ is automatically</span>
- <span class="sd"> detected) and excludes those with ids found in any of the EXCLUDE_FILEs.</span>
- <span class="sd"> If multiple input files are specified, these are treated as paired files.</span>
- <span class="sd"> So if a sequence in one input is excluded, its pair is also excluded from</span>
- <span class="sd"> the same position in all other input files.</span>
- <span class="sd"> If the -k flag is specified, invert the selection to keep instead of exclude.</span>
- <span class="sd"> """</span>
- <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">exclude_files</span><span class="p">,</span> <span class="n">input_files</span><span class="p">,</span> <span class="n">output_files</span><span class="p">,</span> <span class="n">keep</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="s">'exclude'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="s">'-v'</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">keep</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">+=</span> <span class="p">(</span><span class="s">'-k'</span><span class="p">,)</span>
- <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">exclude_files</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">+=</span> <span class="p">(</span><span class="s">'-x'</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span>
- <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">input_files</span><span class="p">[:</span><span class="mi">2</span><span class="p">]:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">+=</span> <span class="p">(</span><span class="s">'-i'</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span>
- <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">[:</span><span class="mi">2</span><span class="p">]:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">+=</span> <span class="p">(</span><span class="s">'-o'</span><span class="p">,</span> <span class="n">o</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
- </div>
- <div class="viewcode-block" id="Fastq2Fasta"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.Fastq2Fasta">[docs]</a><span class="k">class</span> <span class="nc">Fastq2Fasta</span> <span class="p">(</span><span class="n">BaseWrapper</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> usage: fastq2fasta -i FASTQ [...] [-o FASTA ...] [-q QUAL ...] [-a]</span>
- <span class="sd"> [-t OFFSET] [-s SUFFIX]</span>
- <span class="sd"> Converts each FASTQ input file to a FASTA file and quality score file</span>
- <span class="sd"> with the names <basename>.fasta and <basename>.fasta.qual, where <basename></span>
- <span class="sd"> is the name of INPUT up to the last period (or with the names FASTA and QUAL</span>
- <span class="sd"> if specified).</span>
- <span class="sd"> FASTA and QUAL are *appended* to (not truncated).</span>
- <span class="sd"> """</span>
- <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fastq_path</span><span class="p">,</span> <span class="n">fasta_path</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">qual_path</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">suffix</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="s">'fastq2fasta'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="s">'-v'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">+=</span> <span class="p">(</span><span class="s">'-i'</span><span class="p">,</span> <span class="n">fastq_path</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">check_arg</span><span class="p">(</span><span class="s">'-o'</span><span class="p">,</span> <span class="n">fasta_path</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">check_arg</span><span class="p">(</span><span class="s">'-q'</span><span class="p">,</span> <span class="n">qual_path</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">check_arg</span><span class="p">(</span><span class="s">'-s'</span><span class="p">,</span> <span class="n">suffix</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
- </div>
- <div class="viewcode-block" id="Fasta2Fastq"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.Fasta2Fastq">[docs]</a><span class="k">class</span> <span class="nc">Fasta2Fastq</span> <span class="p">(</span><span class="n">BaseWrapper</span><span class="p">):</span>
- <span class="sd">"""</span>
- <span class="sd"> usage: fasta2fastq -i FASTA [...] -q QUAL [...] [-o FASTQ] [-a] [-t OFFSET]</span>
- <span class="sd"> Merges each FASTA file and its corresponding QUAL file into a FASTQ file</span>
- <span class="sd"> with the name <basename>.fastq, where <basename> in the FASTA name up to the</span>
- <span class="sd"> last period (or with name FASTQ if specified).</span>
- <span class="sd"> FASTQ is *appended* to (not truncated).</span>
- <span class="sd"> """</span>
- <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fasta_path</span><span class="p">,</span> <span class="n">qual_path</span><span class="p">,</span> <span class="n">fastq_path</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="s">'fasta2fastq'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="s">'-v'</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">+=</span> <span class="p">(</span><span class="s">'-i'</span><span class="p">,</span> <span class="n">fasta_path</span><span class="p">,</span> <span class="s">'-q'</span><span class="p">,</span> <span class="n">qual_path</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">check_arg</span><span class="p">(</span><span class="s">'-o'</span><span class="p">,</span> <span class="n">fastq_path</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
- </div>
- <div class="viewcode-block" id="FilterIllumina"><a class="viewcode-back" href="../../wrappers.html#biolite.wrappers.FilterIllumina">[docs]</a><span class="k">class</span> <span class="nc">FilterIllum