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  51.   <h1>Source code for biolite.wrappers</h1><div class="highlight"><pre>
    52. 

  52. <span class="c"># BioLite - Tools for processing gene sequence data and automating workflows</span>
    53. 

  53. <span class="c"># Copyright (c) 2012-2013 Brown University. All rights reserved.</span>
    54. 

  54. <span class="c"># </span>
    55. 

  55. <span class="c"># This file is part of BioLite.</span>
    56. 

  56. <span class="c"># </span>
    57. 

  57. <span class="c"># BioLite is free software: you can redistribute it and/or modify</span>
    58. 

  58. <span class="c"># it under the terms of the GNU General Public License as published by</span>
    59. 

  59. <span class="c"># the Free Software Foundation, either version 3 of the License, or</span>
    60. 

  60. <span class="c"># (at your option) any later version.</span>
    61. 

  61. <span class="c"># </span>
    62. 

  62. <span class="c"># BioLite is distributed in the hope that it will be useful,</span>
    63. 

  63. <span class="c"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
    64. 

  64. <span class="c"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
    65. 

  65. <span class="c"># GNU General Public License for more details.</span>
    66. 

  66. <span class="c"># </span>
    67. 

  67. <span class="c"># You should have received a copy of the GNU General Public License</span>
    68. 

  68. <span class="c"># along with BioLite.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
    69. 

  69. 

  70. <span class="sd">&quot;&quot;&quot;</span>
    71. 

  71. <span class="sd">A series of wrappers for external calls to various bioinformatics tools.</span>
    72. 

  72. <span class="sd">&quot;&quot;&quot;</span>
    73. 

  73. 

  74. <span class="kn">import</span> <span class="nn">glob</span>
    75. 

  75. <span class="kn">import</span> <span class="nn">os</span>
    76. 

  76. <span class="kn">import</span> <span class="nn">random</span>
    77. 

  77. <span class="kn">import</span> <span class="nn">shlex</span>
    78. 

  78. <span class="kn">import</span> <span class="nn">subprocess</span>
    79. 

  79. <span class="kn">import</span> <span class="nn">sys</span>
    80. 

  80. 

  81. <span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">namedtuple</span>
    82. 

  82. 

  83. <span class="kn">import</span> <span class="nn">config</span>
    84. 

  84. <span class="kn">import</span> <span class="nn">diagnostics</span>
    85. 

  85. <span class="kn">import</span> <span class="nn">utils</span>
    86. 

  86. 

  87. <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>
    88. 

  88. 	<span class="sd">&quot;&quot;&quot;</span>
    89. 

  89. <span class="sd">	A base class that handles generic wrapper functionality.</span>
    90. 

  90. <span class="sd">	</span>
    91. 

  91. <span class="sd">	Wrappers for specific programs should inherit this class, call `self.init`</span>
    92. 

  92. <span class="sd">	to specify their `name` (which is a key into the executable entries in the</span>
    93. 

  93. <span class="sd">	BioLite configuration file), and append their arguments to the `self.args`</span>
    94. 

  94. <span class="sd">	list.</span>
    95. 

  95. 

  96. <span class="sd">	By convention, a wrapper should call `self.run()` as the final line in its</span>
    97. 

  97. <span class="sd">	`__init__` function. This allows for clean syntax and use of the wrapper</span>
    98. 

  98. <span class="sd">	directly, without assigning it to a variable name, e.g.</span>
    99. 

  99. 

  100. <span class="sd">	wrappers.MyWrapper(arg1, arg2, ...)</span>
    101. 

  101. 

  102. <span class="sd">	When your wrapper runs, BaseWrapper will do the following:</span>
    103. 

  103. 

  104. <span class="sd">	* log the complete command line to diagnostics;</span>
    105. 

  105. <span class="sd">	* optionally call the program with a version flag (invoked with `version`)</span>
    106. 

  106. <span class="sd">	  to obtain a version string, then log this to the :ref:`programs-table`</span>
    107. 

  107. <span class="sd">	  along with a hash of the binary executable file;</span>
    108. 

  108. <span class="sd">	* append the command&#39;s stderr to a file called `name`.log in the CWD;</span>
    109. 

  109. <span class="sd">	* also append the command&#39;s stdout to the same log file, unless you set</span>
    110. 

  110. <span class="sd">	  `self.stdout`, in which case stdout is redirected to a file of that name;</span>
    111. 

  111. <span class="sd">	* on Linux, add a memory profiling library to the LD_PRELOAD environment</span>
    112. 

  112. <span class="sd">	  variable;</span>
    113. 

  113. <span class="sd">	* call the command and check its return code (which should be 0 on success,</span>
    114. 

  114. <span class="sd">	  unless you specify a different code with `self.return_ok`), optionally</span>
    115. 

  115. <span class="sd">	  using the CWD specified in `self.cwd` or the environment specified in</span>
    116. 

  116. <span class="sd">	  `self.env`.</span>
    117. 

  117. <span class="sd">	* parse the stderr of the command to find [biolite.profile] markers and</span>
    118. 

  118. <span class="sd">	  use the rusage values from `utils.safe_call` to populate a profile</span>
    119. 

  119. <span class="sd">	  entity in the diagnostics with walltime, usertime, systime, mem, and</span>
    120. 

  120. <span class="sd">	  vmem attributes.</span>
    121. 

  121. <span class="sd">	&quot;&quot;&quot;</span>
    122. 

  122. 	
    123. 

  123. 	<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>
    124. 

  124. 		<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
    125. 

  125. 		<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>
    126. 

  126. 		<span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">=</span> <span class="p">[]</span>
    127. 

  127. 		<span class="bp">self</span><span class="o">.</span><span class="n">return_ok</span> <span class="o">=</span> <span class="mi">0</span>
    128. 

  128. 		<span class="bp">self</span><span class="o">.</span><span class="n">cwd</span> <span class="o">=</span> <span class="bp">None</span>
    129. 

  129. 		<span class="bp">self</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="bp">None</span>
    130. 

  130. 		<span class="bp">self</span><span class="o">.</span><span class="n">env</span> <span class="o">=</span> <span class="bp">None</span>
    131. 

  131. 		<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>
    132. 

  132. 		<span class="bp">self</span><span class="o">.</span><span class="n">output_patterns</span> <span class="o">=</span> <span class="bp">None</span>
    133. 

  133. 

  134. 

  135. 	<span class="n">init</span> <span class="o">=</span> <span class="n">__init__</span>
    136. 

  136. 	<span class="sd">&quot;&quot;&quot;A shortcut for calling the BaseWrapper __init__ from a subclass.&quot;&quot;&quot;</span>
    137. 

  137. 

  138. 

  139. <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>
    140. 

  140. 		<span class="sd">&quot;&quot;&quot;</span>
    141. 

  141. <span class="sd">		If `value` evaluates to True, append `flag` and `value` to the argument</span>
    142. 

  142. <span class="sd">		list.</span>
    143. 

  143. <span class="sd">		&quot;&quot;&quot;</span>
    144. 

  144. 		<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>
    145. 

  145. 			<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>
    146. 

  146. 			<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>
    147. 

  147. 

  148. </div>
    149. 

  149. <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>
    150. 

  150. 		<span class="sd">&quot;&quot;&quot;</span>
    151. 

  151. <span class="sd">		Indicates that this wrapper should use threading by appending an</span>
    152. 

  152. <span class="sd">		argument with the specified `flag` followed by the number of threads</span>
    153. 

  153. <span class="sd">		specified in the BioLite configuration file.</span>
    154. 

  154. <span class="sd">		&quot;&quot;&quot;</span>
    155. 

  155. 		<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">&#39;threads&#39;</span><span class="p">)),</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_concurrency</span><span class="p">)</span>
    156. 

  156. 		<span class="k">if</span> <span class="n">threads</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
    157. 

  157. 			<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>
    158. 

  158. 			<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>
    159. 

  159. 

  160. </div>
    161. 

  161. <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>
    162. 

  162. 		<span class="sd">&quot;&quot;&quot;</span>
    163. 

  163. <span class="sd">		Indicates that this wrapper should use OpenMP by setting the</span>
    164. 

  164. <span class="sd">		$OMP_NUM_THREADS environment variable equal to the number of threads</span>
    165. 

  165. <span class="sd">		specified in the BioLite configuration file.</span>
    166. 

  166. <span class="sd">		&quot;&quot;&quot;</span>
    167. 

  167. 		<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">&#39;threads&#39;</span><span class="p">)),</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_concurrency</span><span class="p">)</span>
    168. 

  168. 		<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>
    169. 

  169. 		<span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="p">[</span><span class="s">&#39;OMP_NUM_THREADS&#39;</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>
    170. 

  170. 

  171. 	</div>
    172. 

  172. <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>
    173. 

  173. 		<span class="sd">&quot;&quot;&quot;</span>
    174. 

  174. <span class="sd">		Generates and logs a hash to distinguish this particular installation</span>
    175. 

  175. <span class="sd">		of the program (on a certain host, with a certain compiler, program</span>
    176. 

  176. <span class="sd">		version, etc.)</span>
    177. 

  177. 

  178. <span class="sd">		Specify the optional &#39;binary&#39; argument if the wrapper name is not</span>
    179. 

  179. <span class="sd">		actually the program, e.g. if your program has a Perl wrapper script.</span>
    180. 

  180. <span class="sd">		Set &#39;binary&#39; to the binary program that is likely to change between</span>
    181. 

  181. <span class="sd">		versions.</span>
    182. 

  182. 

  183. <span class="sd">		Specify the optional &#39;cmd&#39; argument if the command to run for version</span>
    184. 

  184. <span class="sd">		information is different than what will be invoked by `run` (e.g.</span>
    185. 

  185. <span class="sd">		if the program has a perl wrapper script, but you want to version an</span>
    186. 

  186. <span class="sd">		underlying binary executable).</span>
    187. 

  187. <span class="sd">		&quot;&quot;&quot;</span>
    188. 

  188. 

  189. 		<span class="c"># Setup the command to run.</span>
    190. 

  190. 		<span class="k">if</span> <span class="ow">not</span> <span class="n">cmd</span><span class="p">:</span>
    191. 

  191. 			<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>
    192. 

  192. 		<span class="k">if</span> <span class="n">flag</span><span class="p">:</span>
    193. 

  193. 			<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>
    194. 

  194. 

  195. 		<span class="c"># Run the command.</span>
    196. 

  196. 		<span class="k">try</span><span class="p">:</span>
    197. 

  197. 			<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>
    198. 

  198. 		<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>
    199. 

  199. 			<span class="n">vstring</span> <span class="o">=</span> <span class="n">e</span><span class="o">.</span><span class="n">output</span>
    200. 

  200. 		<span class="k">except</span> <span class="ne">OSError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
    201. 

  201. 			<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>
    202. 

  202. 

  203. 		<span class="k">if</span> <span class="ow">not</span> <span class="n">path</span><span class="p">:</span>
    204. 

  204. 			<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>
    205. 

  205. 

  206. 		<span class="c"># Generate a hash.</span>
    207. 

  207. 		<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>
    208. 

  208. 		<span class="k">if</span> <span class="n">vhash</span><span class="p">:</span>
    209. 

  209. 			<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>
    210. 

  210. 			<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;version&#39;</span><span class="p">,</span> <span class="n">vhash</span><span class="p">)</span>
    211. 

  211. 			<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>
    212. 

  212. 

  213. </div>
    214. 

  214. <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>
    215. 

  215. 		<span class="sd">&quot;&quot;&quot;</span>
    216. 

  216. <span class="sd">		Special case of version() when the executable is a JAR file.</span>
    217. 

  217. <span class="sd">		&quot;&quot;&quot;</span>
    218. 

  218. 		<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">&#39;java&#39;</span><span class="p">)</span>
    219. 

  219. 		<span class="n">cmd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">&#39;-jar&#39;</span><span class="p">)</span>
    220. 

  220. 		<span class="n">cmd</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cmd</span>
    221. 

  221. 		<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>
    222. 

  222. 

  223. </div>
    224. 

  224. <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>
    225. 

  225. 		<span class="sd">&quot;&quot;&quot;</span>
    226. 

  226. <span class="sd">		Call this function at the end of your class&#39;s `__init__` function.</span>
    227. 

  227. <span class="sd">		&quot;&quot;&quot;</span>
    228. 

  228. 		<span class="k">if</span> <span class="ow">not</span> <span class="n">cmd</span><span class="p">:</span>
    229. 

  229. 			<span class="n">cmd</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cmd</span>
    230. 

  230. 		<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;command_executable&#39;</span><span class="p">,</span> <span class="s">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
    231. 

  231. 		<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>
    232. 

  232. 

  233. 		<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>
    234. 

  234. 		<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;command&#39;</span><span class="p">,</span> <span class="s">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
    235. 

  235. 		<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;command_list&#39;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
    236. 

  236. 

  237. 		<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">&#39;.log&#39;</span><span class="p">)</span>
    238. 

  238. 		<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">&#39;a&#39;</span><span class="p">)</span>
    239. 

  239. 		<span class="k">print</span> <span class="o">&gt;&gt;</span> <span class="n">stderr_file</span><span class="p">,</span> <span class="s">&quot;[biolite] timestamp=</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">utils</span><span class="o">.</span><span class="n">timestamp</span><span class="p">()</span>
    240. 

  240. 		<span class="n">stderr_file</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
    241. 

  241. 

  242. 		<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;log&#39;</span><span class="p">,</span> <span class="n">stderr_path</span><span class="p">)</span>
    243. 

  243. 

  244. 		<span class="c"># Write to a stdout file if it was set by the derived class.</span>
    245. 

  245. 		<span class="c"># Otherwise, stdout and stderr will be combined into the log file.</span>
    246. 

  246. 		<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">stdout</span><span class="p">:</span>
    247. 

  247. 			<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">&#39;w&#39;</span><span class="p">)</span>
    248. 

  248. 			<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;stdout&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
    249. 

  249. 		<span class="k">else</span><span class="p">:</span>
    250. 

  250. 			<span class="n">stdout_file</span> <span class="o">=</span> <span class="n">stderr_file</span>
    251. 

  251. 

  252. 		<span class="c"># Setup memory profiling on Linux.</span>
    253. 

  253. 		<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">&#39;Linux&#39;</span><span class="p">:</span>
    254. 

  254. 			<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>
    255. 

  255. 				<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>
    256. 

  256. 			<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">&#39;LD_PRELOAD&#39;</span><span class="p">)</span>
    257. 

  257. 			<span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="p">[</span><span class="s">&#39;LD_PRELOAD&#39;</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">&#39;libmemusage.so&#39;</span><span class="p">)</span>
    258. 

  258. 			<span class="k">if</span> <span class="n">old_preload</span><span class="p">:</span>
    259. 

  259. 				<span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="p">[</span><span class="s">&#39;LD_PRELOAD&#39;</span><span class="p">]</span> <span class="o">+=</span> <span class="s">&quot;:</span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">old_preload</span>
    260. 

  260. 			<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&quot;LD_PRELOAD&quot;</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">&#39;LD_PRELOAD&#39;</span><span class="p">])</span>
    261. 

  261. 

  262. 		<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>
    263. 

  263. 			<span class="n">cmd</span><span class="p">,</span>
    264. 

  264. 			<span class="n">stdout</span><span class="o">=</span><span class="n">stdout_file</span><span class="p">,</span>
    265. 

  265. 			<span class="n">stderr</span><span class="o">=</span><span class="n">stderr_file</span><span class="p">,</span>
    266. 

  266. 			<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>
    267. 

  267. 			<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>
    268. 

  268. 			<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>
    269. 

  269. 

  270. 		<span class="c"># Log profile.</span>
    271. 

  271. 		<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">&#39;profile&#39;</span><span class="p">)</span>
    272. 

  272. 		<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;name&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
    273. 

  273. 		<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;return&#39;</span><span class="p">,</span> <span class="n">retcode</span><span class="p">)</span>
    274. 

  274. 		<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;walltime&#39;</span><span class="p">,</span> <span class="n">walltime</span><span class="p">)</span>
    275. 

  275. 		<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;usertime&#39;</span><span class="p">,</span> <span class="n">rusage</span><span class="o">.</span><span class="n">ru_utime</span><span class="p">)</span>
    276. 

  276. 		<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;systime&#39;</span><span class="p">,</span> <span class="n">rusage</span><span class="o">.</span><span class="n">ru_stime</span><span class="p">)</span>
    277. 

  277. 		<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">&#39;Darwin&#39;</span><span class="p">:</span>
    278. 

  278. 			<span class="n">diagnostics</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="s">&#39;mem&#39;</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>
    279. 

  279. 		<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>
    280. 

  280. 

  281. 		<span class="n">stderr_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
    282. 

  282. 		<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">stdout</span><span class="p">:</span>
    283. 

  283. 			<span class="n">stdout_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
    284. 

  284. 

  285. 		<span class="c"># Reverse any output patterns, since they will be matched against</span>
    286. 

  286. 		<span class="c"># program output from the last line backward.</span>
    287. 

  287. 		<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">output_patterns</span><span class="p">:</span>
    288. 

  288. 			<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>
    289. 

  289. 

  290. 		<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>
    291. 

  291. 		<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>
    292. 

  292. 

  293. </div>
    294. 

  294. <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>
    295. 

  295. 		<span class="sd">&quot;&quot;&quot;</span>
    296. 

  296. <span class="sd">		Special case of run() when the executable is a JAR file.</span>
    297. 

  297. <span class="sd">		&quot;&quot;&quot;</span>
    298. 

  298. 		<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">&#39;java&#39;</span><span class="p">)</span>
    299. 

  299. 		<span class="k">if</span> <span class="n">mem</span><span class="p">:</span>
    300. 

  300. 			<span class="n">cmd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">&#39;-Xmx</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">mem</span><span class="p">)</span>
    301. 

  301. 		<span class="n">cmd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">&#39;-jar&#39;</span><span class="p">)</span>
    302. 

  302. 		<span class="n">cmd</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cmd</span>
    303. 

  303. 		<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>
    304. 

  304. 

  305. </div></div>
    306. 

  306. <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>
    307. 

  307. 	<span class="sd">&quot;&quot;&quot;</span>
    308. 

  308. <span class="sd">	For tools that need insert sizes, use available estimates from the</span>
    309. 

  309. <span class="sd">	diagnostics database, or resort to the default values in the BioLite</span>
    310. 

  310. <span class="sd">	configuration file.</span>
    311. 

  311. 

  312. <span class="sd">	Returns an AttributeDict with the fields `mean`, `stddev` and `max`.</span>
    313. 

  313. <span class="sd">	&quot;&quot;&quot;</span>
    314. 

  314. 	<span class="n">entity</span> <span class="o">=</span> <span class="n">diagnostics</span><span class="o">.</span><span class="n">INSERT_SIZE</span>
    315. 

  315. 	<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>
    316. 

  316. 	<span class="c"># Try the diagnostics cache, if the estimate is from an earlier stage</span>
    317. 

  317. 	<span class="c"># of the current pipeline.</span>
    318. 

  318. 	<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">&#39;mean&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
    319. 

  319. 	<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">&#39;stddev&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
    320. 

  320. 	<span class="n">size</span><span class="o">.</span><span class="n">max</span> <span class="o">=</span> <span class="mi">0</span>
    321. 

  321. 	<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>
    322. 

  322. 		<span class="c"># Search the global diagnostics database (passing None to lookup_by_id</span>
    323. 

  323. 		<span class="c"># will use the currently initialized id in diagnostics.</span>
    324. 

  324. 		<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>
    325. 

  325. 		<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">&#39;mean&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
    326. 

  326. 		<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">&#39;stddev&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
    327. 

  327. 	<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>
    328. 

  328. 		<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">&#39;max_insert_size&#39;</span><span class="p">))</span>
    329. 

  329. 		<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">&#39;mean_insert_size&#39;</span><span class="p">))</span>
    330. 

  330. 	<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>
    331. 

  331. 		<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> \
    332. 

  332. 					<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">&#39;max_insert_stddev&#39;</span><span class="p">))</span>
    333. 

  333. 	<span class="k">return</span> <span class="n">size</span>
    334. 

  334. 

  335. 

  336. <span class="c">### BioLite command line tools ###</span>
    337. 

  337. </div>
    338. 

  338. <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>
    339. 

  339. 	<span class="sd">&quot;&quot;&quot;</span>
    340. 

  340. <span class="sd">	usage: count_lines [-t THREADS] [INPUT ...]</span>
    341. 

  341. 

  342. <span class="sd">	Count the number of lines in the INPUT files using multiple threads to</span>
    343. 

  343. <span class="sd">	increase throughput.</span>
    344. 

  344. <span class="sd">	&quot;&quot;&quot;</span>
    345. 

  345. 

  346. 	<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>
    347. 

  347. 		<span class="bp">self</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="s">&#39;count_lines&#39;</span><span class="p">)</span>
    348. 

  348. 		<span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="s">&#39;-v&#39;</span><span class="p">)</span>
    349. 

  349. 		<span class="bp">self</span><span class="o">.</span><span class="n">add_threading</span><span class="p">(</span><span class="s">&#39;-t&#39;</span><span class="p">)</span>
    350. 

  350. 		<span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">+=</span> <span class="n">inputs</span>
    351. 

  351. 		<span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
    352. 

  352. 

  353. </div>
    354. 

  354. <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>
    355. 

  355. 	<span class="sd">&quot;&quot;&quot;</span>
    356. 

  356. <span class="sd">	usage: coverage [-i SAM] [-o STATS]</span>
    357. 

  357. 

  358. <span class="sd">	Parses a SAM alignment file and writes a coverage table to STATS with</span>
    359. 

  359. <span class="sd">	columns for the reference name, the length of the referene, and the number</span>
    360. 

  360. <span class="sd">	of reads covering it in the alignment.</span>
    361. 

  361. <span class="sd">	&quot;&quot;&quot;</span>
    362. 

  362. 

  363. 	<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>
    364. 

  364. 		<span class="bp">self</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="s">&#39;coverage&#39;</span><span class="p">)</span>
    365. 

  365. 		<span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="s">&#39;-v&#39;</span><span class="p">)</span>
    366. 

  366. 		<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">&#39;-i&#39;</span><span class="p">,</span> <span class="n">sam</span><span class="p">)</span>
    367. 

  367. 		<span class="bp">self</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="n">stats</span>
    368. 

  368. 		<span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
    369. 

  369. 

  370. </div>
    371. 

  371. <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>
    372. 

  372. 	<span class="sd">&quot;&quot;&quot;</span>
    373. 

  373. <span class="sd">	usage: exclude -x EXCLUDE_FILE [-k] [...] [-i INPUT ...] [-o OUTPUT ...]</span>
    374. 

  374. 

  375. <span class="sd">	Filters all the reads in the input files (FASTA or FASTQ is automatically</span>
    376. 

  376. <span class="sd">	detected) and excludes those with ids found in any of the EXCLUDE_FILEs.</span>
    377. 

  377. 

  378. <span class="sd">	If multiple input files are specified, these are treated as paired files.</span>
    379. 

  379. <span class="sd">	So if a sequence in one input is excluded, its pair is also excluded from</span>
    380. 

  380. <span class="sd">	the same position in all other input files.</span>
    381. 

  381. 

  382. <span class="sd">	If the -k flag is specified, invert the selection to keep instead of exclude.</span>
    383. 

  383. <span class="sd">	&quot;&quot;&quot;</span>
    384. 

  384. 

  385. 	<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>
    386. 

  386. 		<span class="bp">self</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="s">&#39;exclude&#39;</span><span class="p">)</span>
    387. 

  387. 		<span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="s">&#39;-v&#39;</span><span class="p">)</span>
    388. 

  388. 		<span class="k">if</span> <span class="n">keep</span><span class="p">:</span>
    389. 

  389. 			<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">&#39;-k&#39;</span><span class="p">,)</span>
    390. 

  390. 		<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>
    391. 

  391. 			<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">&#39;-x&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span>
    392. 

  392. 		<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>
    393. 

  393. 			<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">&#39;-i&#39;</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span>
    394. 

  394. 		<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>
    395. 

  395. 			<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">&#39;-o&#39;</span><span class="p">,</span> <span class="n">o</span><span class="p">)</span>
    396. 

  396. 		<span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
    397. 

  397. 

  398. </div>
    399. 

  399. <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>
    400. 

  400. 	<span class="sd">&quot;&quot;&quot;</span>
    401. 

  401. <span class="sd">	usage: fastq2fasta -i FASTQ [...] [-o FASTA ...] [-q QUAL ...] [-a]</span>
    402. 

  402. <span class="sd">	                   [-t OFFSET] [-s SUFFIX]</span>
    403. 

  403. 

  404. <span class="sd">	Converts each FASTQ input file to a FASTA file and quality score file</span>
    405. 

  405. <span class="sd">	with the names &lt;basename&gt;.fasta and &lt;basename&gt;.fasta.qual, where &lt;basename&gt;</span>
    406. 

  406. <span class="sd">	is the name of INPUT up to the last period (or with the names FASTA and QUAL</span>
    407. 

  407. <span class="sd">	if specified).</span>
    408. 

  408. 

  409. <span class="sd">	FASTA and QUAL are *appended* to (not truncated).</span>
    410. 

  410. <span class="sd">	&quot;&quot;&quot;</span>
    411. 

  411. 

  412. 	<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>
    413. 

  413. 		<span class="bp">self</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="s">&#39;fastq2fasta&#39;</span><span class="p">)</span>
    414. 

  414. 		<span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="s">&#39;-v&#39;</span><span class="p">)</span>
    415. 

  415. 		<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">&#39;-i&#39;</span><span class="p">,</span> <span class="n">fastq_path</span><span class="p">)</span>
    416. 

  416. 		<span class="bp">self</span><span class="o">.</span><span class="n">check_arg</span><span class="p">(</span><span class="s">&#39;-o&#39;</span><span class="p">,</span> <span class="n">fasta_path</span><span class="p">)</span>
    417. 

  417. 		<span class="bp">self</span><span class="o">.</span><span class="n">check_arg</span><span class="p">(</span><span class="s">&#39;-q&#39;</span><span class="p">,</span> <span class="n">qual_path</span><span class="p">)</span>
    418. 

  418. 		<span class="bp">self</span><span class="o">.</span><span class="n">check_arg</span><span class="p">(</span><span class="s">&#39;-s&#39;</span><span class="p">,</span> <span class="n">suffix</span><span class="p">)</span>
    419. 

  419. 		<span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
    420. 

  420. 

  421. </div>
    422. 

  422. <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>
    423. 

  423. 	<span class="sd">&quot;&quot;&quot;</span>
    424. 

  424. <span class="sd">	usage: fasta2fastq -i FASTA [...] -q QUAL [...] [-o FASTQ] [-a] [-t OFFSET]</span>
    425. 

  425. 

  426. <span class="sd">	Merges each FASTA file and its corresponding QUAL file into a FASTQ file</span>
    427. 

  427. <span class="sd">	with the name &lt;basename&gt;.fastq, where &lt;basename&gt; in the FASTA name up to the</span>
    428. 

  428. <span class="sd">	last period (or with name FASTQ if specified).</span>
    429. 

  429. 

  430. <span class="sd">	FASTQ is *appended* to (not truncated).</span>
    431. 

  431. <span class="sd">	&quot;&quot;&quot;</span>
    432. 

  432. 

  433. 	<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>
    434. 

  434. 		<span class="bp">self</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="s">&#39;fasta2fastq&#39;</span><span class="p">)</span>
    435. 

  435. 		<span class="bp">self</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="s">&#39;-v&#39;</span><span class="p">)</span>
    436. 

  436. 		<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">&#39;-i&#39;</span><span class="p">,</span> <span class="n">fasta_path</span><span class="p">,</span> <span class="s">&#39;-q&#39;</span><span class="p">,</span> <span class="n">qual_path</span><span class="p">)</span>
    437. 

  437. 		<span class="bp">self</span><span class="o">.</span><span class="n">check_arg</span><span class="p">(</span><span class="s">&#39;-o&#39;</span><span class="p">,</span> <span class="n">fastq_path</span><span class="p">)</span>
    438. 

  438. 		<span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
    439. 

  439. 

  440. </div>
    441. 

  441. <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
    442.