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  <div class="section" id="input-and-options-of-macsyfinder">
<span id="input"></span><h1>Input and Options of MacSyFinder<a class="headerlink" href="#input-and-options-of-macsyfinder" title="Permalink to this headline"></a></h1>
<div class="section" id="input-dataset">
<span id="input-dataset-label"></span><h2>Input dataset<a class="headerlink" href="#input-dataset" title="Permalink to this headline"></a></h2>
<p>The input dataset must be a set of protein sequences in <strong>Fasta format</strong> (see <a class="reference external" href="http://en.wikipedia.org/wiki/FASTA_format">http://en.wikipedia.org/wiki/FASTA_format</a>).</p>
<p>The <a class="reference internal" href="#config-base-label"><span class="std std-ref">base section</span></a> in the configuration file (see <a class="reference internal" href="#config-definition-label"><span class="std std-ref">Configuration file</span></a>) can be used to specify <strong>the path</strong> and the <strong>type of dataset</strong> to deal with, as well as the <cite>&#8211;sequence_db</cite> and <cite>&#8211;db_type</cite> parameters respectively, described in the <a class="reference internal" href="#command-line-label"><span class="std std-ref">Command-line options</span></a> (see <a class="reference internal" href="#cmd-input-label"><span class="std std-ref">Input options</span></a>).</p>
<blockquote>
<div><p>Four types of protein datasets are supported:</p>
<blockquote>
<div><ul class="simple">
<li><em>unordered</em> : a set of sequences (<em>e.g.</em> a metagenomic dataset)</li>
<li><em>unordered_replicon</em> : a set of sequences corresponding to a complete genome (<em>e.g.</em> an unassembled complete genome)</li>
<li><em>ordered_replicon</em> : a set of sequences corresponding to an ordered complete replicon (<em>e.g.</em> an assembled complete genome)</li>
<li><em>gembase</em> : a set of multiple ordered replicons, which format follows the convention described in <a class="reference internal" href="gembase_convention.html#gembase-convention"><span class="std std-ref">Gembase format</span></a>.</li>
</ul>
</div></blockquote>
</div></blockquote>
<p>For &#8220;ordered&#8221; (&#8220;ordered_replicon&#8221; or &#8220;gembase&#8221;) datasets only, MacSyFinder can take into account the <strong>shape of the genome</strong>: &#8220;linear&#8221;, or &#8220;circular&#8221; for detection. The default is set to &#8220;circular&#8221;.</p>
<blockquote>
<div><p>This can be set with the <cite>&#8211;replicon_topology</cite> parameter from <a class="reference internal" href="#command-line-label"><span class="std std-ref">Command-line options</span></a> (see <a class="reference internal" href="#cmd-input-label"><span class="std std-ref">Input options</span></a>), or in the configuration in the <a class="reference internal" href="#config-base-label"><span class="std std-ref">base section</span></a>.</p>
<p>With the &#8220;gembase&#8221; format, it is possible to specify a topology per replicon with a topology file (see <a class="reference internal" href="gembase_convention.html#gembase-convention"><span class="std std-ref">Gembase format</span></a> and <a class="reference internal" href="gembase_convention.html#topology-files"><span class="std std-ref">Topology files</span></a>).</p>
</div></blockquote>
</div>
<div class="section" id="command-line-options">
<span id="command-line-label"></span><h2>Command-line options<a class="headerlink" href="#command-line-options" title="Permalink to this headline"></a></h2>
<p>Positional arguments:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">systems</span>               <span class="n">The</span> <span class="n">systems</span> <span class="n">to</span> <span class="n">detect</span><span class="o">.</span> <span class="n">This</span> <span class="ow">is</span> <span class="n">an</span> <span class="n">obligatory</span> <span class="n">option</span>
                      <span class="k">with</span> <span class="n">no</span> <span class="n">keyword</span> <span class="n">associated</span> <span class="n">to</span> <span class="n">it</span><span class="o">.</span> <span class="n">To</span> <span class="n">detect</span> <span class="nb">all</span> <span class="n">systems</span>
                      <span class="n">described</span> <span class="ow">in</span> <span class="o">.</span><span class="n">xml</span> <span class="n">available</span><span class="p">,</span> <span class="nb">set</span> <span class="n">to</span> <span class="s2">&quot;all&quot;</span> <span class="p">(</span><span class="n">case</span> <span class="n">insensitive</span><span class="p">)</span><span class="o">.</span>
                      <span class="n">Otherwise</span><span class="p">,</span> <span class="n">a</span> <span class="n">single</span> <span class="ow">or</span> <span class="n">multiple</span> <span class="n">systems</span> <span class="n">can</span> <span class="n">be</span> <span class="n">specified</span><span class="o">.</span>
                      <span class="n">For</span> <span class="n">example</span><span class="p">:</span> <span class="s2">&quot;SystemA SystemB&quot;</span><span class="o">.</span>
</pre></div>
</div>
<p>Optional arguments:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">-</span><span class="n">h</span><span class="p">,</span> <span class="o">--</span><span class="n">help</span>            <span class="n">Show</span> <span class="n">the</span> <span class="n">help</span> <span class="n">message</span> <span class="ow">and</span> <span class="n">exit</span>
</pre></div>
</div>
<p id="cmd-input-label">Input dataset options:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">--</span><span class="n">sequence</span><span class="o">-</span><span class="n">db</span> <span class="n">SEQUENCE_DB</span>
                      <span class="n">Path</span> <span class="n">to</span> <span class="n">the</span> <span class="n">sequence</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="n">fasta</span> <span class="nb">format</span><span class="o">.</span>

<span class="o">--</span><span class="n">db</span><span class="o">-</span><span class="nb">type</span> <span class="p">{</span><span class="n">unordered_replicon</span><span class="p">,</span><span class="n">ordered_replicon</span><span class="p">,</span><span class="n">gembase</span><span class="p">,</span><span class="n">unordered</span><span class="p">}</span>
                      <span class="n">The</span> <span class="nb">type</span> <span class="n">of</span> <span class="n">dataset</span> <span class="n">to</span> <span class="n">deal</span> <span class="k">with</span><span class="o">.</span> <span class="s2">&quot;unordered_replicon&quot;</span>
                      <span class="n">corresponds</span> <span class="n">to</span> <span class="n">a</span> <span class="n">non</span><span class="o">-</span><span class="n">assembled</span> <span class="n">genome</span><span class="p">,</span> <span class="s2">&quot;unordered&quot;</span> <span class="n">to</span>
                      <span class="n">a</span> <span class="n">metagenomic</span> <span class="n">dataset</span><span class="p">,</span> <span class="s2">&quot;ordered_replicon&quot;</span> <span class="n">to</span> <span class="n">an</span>
                      <span class="n">assembled</span> <span class="n">genome</span><span class="p">,</span> <span class="ow">and</span> <span class="s2">&quot;gembase&quot;</span> <span class="n">to</span> <span class="n">a</span> <span class="nb">set</span> <span class="n">of</span> <span class="n">replicons</span>
                      <span class="n">where</span> <span class="n">sequence</span> <span class="n">identifiers</span> <span class="n">follow</span> <span class="n">this</span> <span class="n">convention</span><span class="p">:</span>
                      <span class="s2">&quot;&gt;RepliconName_SequenceID&quot;</span>

<span class="o">--</span><span class="n">replicon</span><span class="o">-</span><span class="n">topology</span> <span class="p">{</span><span class="n">linear</span><span class="p">,</span><span class="n">circular</span><span class="p">}</span>
                      <span class="n">The</span> <span class="n">topology</span> <span class="n">of</span> <span class="n">the</span> <span class="n">replicons</span> <span class="p">(</span><span class="n">this</span> <span class="n">option</span> <span class="ow">is</span>
                      <span class="n">meaningful</span> <span class="n">only</span> <span class="k">if</span> <span class="n">the</span> <span class="n">db_type</span> <span class="ow">is</span> <span class="s1">&#39;ordered_replicon&#39;</span>
                      <span class="ow">or</span> <span class="s1">&#39;gembase&#39;</span>

<span class="o">--</span><span class="n">topology</span><span class="o">-</span><span class="n">file</span> <span class="n">TOPOLOGY</span><span class="o">-</span><span class="n">FILE</span>
                      <span class="n">Topology</span> <span class="n">file</span> <span class="n">path</span><span class="o">.</span> <span class="n">The</span> <span class="n">topology</span> <span class="n">file</span> <span class="n">allows</span> <span class="n">to</span>
                      <span class="n">specify</span> <span class="n">a</span> <span class="n">topology</span> <span class="p">(</span><span class="n">linear</span> <span class="ow">or</span> <span class="n">circular</span><span class="p">)</span> <span class="k">for</span> <span class="n">each</span>
                      <span class="n">replicon</span> <span class="p">(</span><span class="n">this</span> <span class="n">option</span> <span class="ow">is</span> <span class="n">meaningful</span> <span class="n">only</span> <span class="k">if</span> <span class="n">the</span>
                      <span class="n">db_type</span> <span class="ow">is</span> <span class="s1">&#39;ordered_replicon&#39;</span> <span class="ow">or</span> <span class="s1">&#39;gembase&#39;</span><span class="o">.</span> <span class="n">A</span> <span class="n">topology</span>
                      <span class="n">file</span> <span class="ow">is</span> <span class="n">a</span> <span class="n">tabular</span> <span class="n">file</span> <span class="k">with</span> <span class="n">two</span> <span class="n">columns</span><span class="p">:</span> <span class="n">the</span> <span class="mi">1</span><span class="n">st</span> <span class="ow">is</span>
                      <span class="n">the</span> <span class="n">replicon</span> <span class="n">name</span><span class="p">,</span> <span class="ow">and</span> <span class="n">the</span> <span class="mi">2</span><span class="n">nd</span> <span class="n">the</span> <span class="n">corresponding</span>
                      <span class="n">topology</span><span class="p">:</span> <span class="s2">&quot;RepliconA linear&quot;</span>

<span class="o">--</span><span class="n">idx</span>                 <span class="n">Forces</span> <span class="n">to</span> <span class="n">build</span> <span class="n">the</span> <span class="n">indexes</span> <span class="k">for</span> <span class="n">the</span> <span class="n">sequence</span> <span class="n">dataset</span>
                      <span class="n">even</span> <span class="k">if</span> <span class="n">they</span> <span class="n">were</span> <span class="n">presviously</span> <span class="n">computed</span> <span class="ow">and</span> <span class="n">present</span> <span class="n">at</span>
                      <span class="n">the</span> <span class="n">dataset</span> <span class="n">location</span> <span class="p">(</span><span class="n">default</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
</pre></div>
</div>
<p id="system-detect-options">Systems detection options:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">--</span><span class="n">inter</span><span class="o">-</span><span class="n">gene</span><span class="o">-</span><span class="nb">max</span><span class="o">-</span><span class="n">space</span> <span class="n">SYSTEM</span> <span class="n">VALUE</span>
                      <span class="n">Co</span><span class="o">-</span><span class="n">localization</span> <span class="n">criterion</span><span class="p">:</span> <span class="n">maximum</span> <span class="n">number</span> <span class="n">of</span>
                      <span class="n">components</span> <span class="n">non</span><span class="o">-</span><span class="n">matched</span> <span class="n">by</span> <span class="n">a</span> <span class="n">profile</span> <span class="n">allowed</span> <span class="n">between</span>
                      <span class="n">two</span> <span class="n">matched</span> <span class="n">components</span> <span class="k">for</span> <span class="n">them</span> <span class="n">to</span> <span class="n">be</span> <span class="n">considered</span>
                      <span class="n">contiguous</span><span class="o">.</span> <span class="n">Option</span> <span class="n">only</span> <span class="n">meaningful</span> <span class="k">for</span> <span class="s1">&#39;ordered&#39;</span>
                      <span class="n">datasets</span><span class="o">.</span> <span class="n">The</span> <span class="n">first</span> <span class="n">value</span> <span class="n">must</span> <span class="n">match</span> <span class="n">a</span> <span class="n">system</span> <span class="n">name</span><span class="p">,</span>
                      <span class="n">the</span> <span class="n">second</span> <span class="n">a</span> <span class="n">number</span> <span class="n">of</span> <span class="n">components</span><span class="o">.</span> <span class="n">This</span> <span class="n">option</span> <span class="n">can</span> <span class="n">be</span>
                      <span class="n">repeated</span> <span class="n">several</span> <span class="n">times</span><span class="p">:</span>
                      <span class="s2">&quot;--inter-gene-max-space T3SS 12 --inter-gene-max-space Flagellum 20&quot;</span>

<span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">mandatory</span><span class="o">-</span><span class="n">genes</span><span class="o">-</span><span class="n">required</span> <span class="n">SYSTEM</span> <span class="n">VALUE</span>
                      <span class="n">The</span> <span class="n">minimal</span> <span class="n">number</span> <span class="n">of</span> <span class="n">mandatory</span> <span class="n">genes</span> <span class="n">required</span> <span class="k">for</span>
                      <span class="n">system</span> <span class="n">assessment</span><span class="o">.</span> <span class="n">The</span> <span class="n">first</span> <span class="n">value</span> <span class="n">must</span> <span class="n">correspond</span> <span class="n">to</span>
                      <span class="n">a</span> <span class="n">system</span> <span class="n">name</span><span class="p">,</span> <span class="n">the</span> <span class="n">second</span> <span class="n">value</span> <span class="n">to</span> <span class="n">an</span> <span class="n">integer</span><span class="o">.</span> <span class="n">This</span>
                      <span class="n">option</span> <span class="n">can</span> <span class="n">be</span> <span class="n">repeated</span> <span class="n">several</span> <span class="n">times</span><span class="p">:</span>
                      <span class="s2">&quot;--min-mandatory-genes-required T2SS 15</span>
                      <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">mandatory</span><span class="o">-</span><span class="n">genes</span><span class="o">-</span><span class="n">required</span> <span class="n">Flagellum</span> <span class="mi">10</span><span class="s2">&quot;</span>

<span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">genes</span><span class="o">-</span><span class="n">required</span> <span class="n">SYSTEM</span> <span class="n">VALUE</span>
                      <span class="n">The</span> <span class="n">minimal</span> <span class="n">number</span> <span class="n">of</span> <span class="n">genes</span> <span class="n">required</span> <span class="k">for</span> <span class="n">system</span>
                      <span class="n">assessment</span> <span class="p">(</span><span class="n">includes</span> <span class="n">both</span> <span class="s1">&#39;mandatory&#39;</span> <span class="ow">and</span> <span class="s1">&#39;accessory&#39;</span>
                      <span class="n">components</span><span class="p">)</span><span class="o">.</span> <span class="n">The</span> <span class="n">first</span> <span class="n">value</span> <span class="n">must</span> <span class="n">correspond</span> <span class="n">to</span> <span class="n">a</span>
                      <span class="n">system</span> <span class="n">name</span><span class="p">,</span> <span class="n">the</span> <span class="n">second</span> <span class="n">value</span> <span class="n">to</span> <span class="n">an</span> <span class="n">integer</span><span class="o">.</span> <span class="n">This</span>
                      <span class="n">option</span> <span class="n">can</span> <span class="n">be</span> <span class="n">repeated</span> <span class="n">several</span> <span class="n">times</span><span class="p">:</span>
                      <span class="s2">&quot;--min-genes-required T2SS 15 --min-genes-required Flagellum 10&quot;</span>

<span class="o">--</span><span class="nb">max</span><span class="o">-</span><span class="n">nb</span><span class="o">-</span><span class="n">genes</span> <span class="n">SYSTEM</span> <span class="n">VALUE</span>
                      <span class="n">The</span> <span class="n">maximal</span> <span class="n">number</span> <span class="n">of</span> <span class="n">genes</span> <span class="n">allowed</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">system</span><span class="o">.</span>

<span class="o">--</span><span class="n">multi</span><span class="o">-</span><span class="n">loci</span> <span class="n">SYSTEM</span>
                      <span class="n">Specifies</span> <span class="k">if</span> <span class="n">the</span> <span class="n">system</span> <span class="n">can</span> <span class="n">be</span> <span class="n">detected</span> <span class="k">as</span> <span class="n">a</span> <span class="s1">&#39;scattered&#39;</span>
                      <span class="n">system</span><span class="o">.</span> <span class="p">(</span><span class="n">default</span><span class="p">:</span> <span class="kc">False</span><span class="p">)</span>
</pre></div>
</div>
<p id="hmmer-options">Options for Hmmer execution and hits filtering:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">--</span><span class="n">hmmer</span> <span class="n">HMMER_EXE</span>     <span class="n">Path</span> <span class="n">to</span> <span class="n">the</span> <span class="n">Hmmer</span> <span class="n">program</span><span class="o">.</span>

<span class="o">--</span><span class="n">index</span><span class="o">-</span><span class="n">db</span> <span class="n">INDEX_DB_EXE</span>
                      <span class="n">The</span> <span class="n">indexer</span> <span class="n">to</span> <span class="n">be</span> <span class="n">used</span> <span class="k">for</span> <span class="n">Hmmer</span><span class="o">.</span> <span class="n">The</span> <span class="n">value</span> <span class="n">can</span> <span class="n">be</span>
                      <span class="n">either</span> <span class="s1">&#39;makeblastdb&#39;</span> <span class="ow">or</span> <span class="s1">&#39;formatdb&#39;</span> <span class="ow">or</span> <span class="n">the</span> <span class="n">path</span> <span class="n">to</span> <span class="n">one</span>
                      <span class="n">of</span> <span class="n">these</span> <span class="n">binary</span> <span class="p">(</span><span class="n">default</span> <span class="o">=</span> <span class="n">makeblastb</span><span class="p">)</span><span class="o">.</span>

<span class="o">--</span><span class="n">e</span><span class="o">-</span><span class="n">value</span><span class="o">-</span><span class="n">search</span> <span class="n">E_VALUE_RES</span>
                      <span class="n">Maximal</span> <span class="n">e</span><span class="o">-</span><span class="n">value</span> <span class="k">for</span> <span class="n">hits</span> <span class="n">to</span> <span class="n">be</span> <span class="n">reported</span> <span class="n">during</span> <span class="n">Hmmer</span>
                      <span class="n">search</span><span class="o">.</span> <span class="p">(</span><span class="n">default</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>

<span class="o">--</span><span class="n">i</span><span class="o">-</span><span class="n">evalue</span><span class="o">-</span><span class="n">select</span> <span class="n">I_EVALUE_SEL</span>
                      <span class="n">Maximal</span> <span class="n">independent</span> <span class="n">e</span><span class="o">-</span><span class="n">value</span> <span class="k">for</span> <span class="n">Hmmer</span> <span class="n">hits</span> <span class="n">to</span> <span class="n">be</span>
                      <span class="n">selected</span> <span class="k">for</span> <span class="n">system</span> <span class="n">detection</span><span class="o">.</span> <span class="p">(</span><span class="n">default</span> <span class="o">=</span> <span class="mf">0.001</span><span class="p">)</span>

<span class="o">--</span><span class="n">coverage</span><span class="o">-</span><span class="n">profile</span> <span class="n">COVERAGE_PROFILE</span>
                      <span class="n">Minimal</span> <span class="n">profile</span> <span class="n">coverage</span> <span class="n">required</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">hit</span> <span class="n">alignment</span>
                      <span class="n">to</span> <span class="n">allow</span> <span class="n">the</span> <span class="n">hit</span> <span class="n">selection</span> <span class="k">for</span> <span class="n">system</span> <span class="n">detection</span><span class="o">.</span>
                      <span class="p">(</span><span class="n">default</span> <span class="o">=</span> <span class="mf">0.5</span><span class="p">)</span>
</pre></div>
</div>
<p>Path options:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">-</span><span class="n">d</span> <span class="n">DEF_DIR</span><span class="p">,</span> <span class="o">--</span><span class="k">def</span> <span class="nf">DEF_DIR</span>
                      <span class="n">Path</span> <span class="n">to</span> <span class="n">the</span> <span class="n">systems</span> <span class="n">definition</span> <span class="n">files</span><span class="o">.</span>

<span class="o">-</span><span class="n">r</span> <span class="n">RES_SEARCH_DIR</span><span class="p">,</span> <span class="o">--</span><span class="n">res</span><span class="o">-</span><span class="n">search</span><span class="o">-</span><span class="nb">dir</span> <span class="n">RES_SEARCH_DIR</span>
                      <span class="n">Path</span> <span class="n">to</span> <span class="n">the</span> <span class="n">directory</span> <span class="n">where</span> <span class="n">to</span> <span class="n">store</span> <span class="n">MacSyFinder</span> <span class="n">search</span>
                      <span class="n">results</span> <span class="n">directories</span><span class="o">.</span>

<span class="o">--</span><span class="n">res</span><span class="o">-</span><span class="n">search</span><span class="o">-</span><span class="n">suffix</span> <span class="n">RES_SEARCH_SUFFIX</span>
                      <span class="n">The</span> <span class="n">suffix</span> <span class="n">to</span> <span class="n">give</span> <span class="n">to</span> <span class="n">Hmmer</span> <span class="n">raw</span> <span class="n">output</span> <span class="n">files</span><span class="o">.</span>

<span class="o">--</span><span class="n">res</span><span class="o">-</span><span class="n">extract</span><span class="o">-</span><span class="n">suffix</span> <span class="n">RES_EXTRACT_SUFFIX</span>
                      <span class="n">The</span> <span class="n">suffix</span> <span class="n">to</span> <span class="n">give</span> <span class="n">to</span> <span class="n">filtered</span> <span class="n">hits</span> <span class="n">output</span> <span class="n">files</span><span class="o">.</span>

<span class="o">-</span><span class="n">p</span> <span class="n">PROFILE_DIR</span><span class="p">,</span> <span class="o">--</span><span class="n">profile</span><span class="o">-</span><span class="nb">dir</span> <span class="n">PROFILE_DIR</span>
                      <span class="n">Path</span> <span class="n">to</span> <span class="n">the</span> <span class="n">profiles</span> <span class="n">directory</span><span class="o">.</span>

<span class="o">--</span><span class="n">profile</span><span class="o">-</span><span class="n">suffix</span> <span class="n">PROFILE_SUFFIX</span>
                      <span class="n">The</span> <span class="n">suffix</span> <span class="n">of</span> <span class="n">profile</span> <span class="n">files</span><span class="o">.</span> <span class="n">For</span> <span class="n">each</span> <span class="s1">&#39;Gene&#39;</span> <span class="n">element</span><span class="p">,</span>
                      <span class="n">the</span> <span class="n">corresponding</span> <span class="n">profile</span> <span class="ow">is</span> <span class="n">searched</span> <span class="ow">in</span> <span class="n">the</span>
                      <span class="s1">&#39;profile_dir&#39;</span><span class="p">,</span> <span class="ow">in</span> <span class="n">a</span> <span class="n">file</span> <span class="n">which</span> <span class="n">name</span> <span class="ow">is</span> <span class="n">based</span> <span class="n">on</span> <span class="n">the</span>
                      <span class="n">Gene</span> <span class="n">name</span> <span class="o">+</span> <span class="n">the</span> <span class="n">profile</span> <span class="n">suffix</span><span class="o">.</span> <span class="n">For</span> <span class="n">instance</span><span class="p">,</span> <span class="k">if</span> <span class="n">the</span>
                      <span class="n">Gene</span> <span class="ow">is</span> <span class="n">named</span> <span class="s1">&#39;gspG&#39;</span> <span class="ow">and</span> <span class="n">the</span> <span class="n">suffix</span> <span class="ow">is</span> <span class="s1">&#39;.hmm3&#39;</span><span class="p">,</span> <span class="n">then</span>
                      <span class="n">the</span> <span class="n">profile</span> <span class="n">should</span> <span class="n">be</span> <span class="n">placed</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">specified</span> <span class="n">folder</span>
                      <span class="s1">&#39;profile_dir&#39;</span> <span class="ow">and</span> <span class="n">be</span> <span class="n">named</span> <span class="s1">&#39;gspG.hmm3&#39;</span><span class="o">.</span>
                      <span class="p">(</span><span class="n">default</span><span class="p">:</span> <span class="s2">&quot;.hmm&quot;</span><span class="p">)</span>
</pre></div>
</div>
<p>General options:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">-</span><span class="n">w</span> <span class="n">WORKER_NB</span><span class="p">,</span> <span class="o">--</span><span class="n">worker</span> <span class="n">WORKER_NB</span>
                      <span class="n">Number</span> <span class="n">of</span> <span class="n">workers</span> <span class="n">to</span> <span class="n">be</span> <span class="n">used</span> <span class="n">by</span> <span class="n">MacSyFinder</span><span class="o">.</span> <span class="n">In</span> <span class="n">the</span> <span class="n">case</span>
                      <span class="n">the</span> <span class="n">user</span> <span class="n">wants</span> <span class="n">to</span> <span class="n">run</span> <span class="n">MacSyFinder</span> <span class="ow">in</span> <span class="n">a</span> <span class="n">multi</span><span class="o">-</span><span class="n">thread</span> <span class="n">mode</span><span class="o">.</span>
                      <span class="n">All</span> <span class="n">workers</span> <span class="n">can</span> <span class="n">be</span> <span class="n">used</span> <span class="k">with</span> <span class="n">the</span> <span class="n">value</span> <span class="s1">&#39;0&#39;</span><span class="o">.</span> <span class="p">(</span><span class="n">default</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>

<span class="o">-</span><span class="n">v</span><span class="p">,</span> <span class="o">--</span><span class="n">verbosity</span>       <span class="n">Increases</span> <span class="n">the</span> <span class="n">verbosity</span> <span class="n">level</span><span class="o">.</span> <span class="n">There</span> <span class="n">are</span> <span class="mi">4</span> <span class="n">levels</span><span class="p">:</span>
                      <span class="n">Error</span> <span class="n">messages</span> <span class="p">(</span><span class="n">default</span><span class="p">),</span> <span class="ne">Warning</span> <span class="p">(</span><span class="o">-</span><span class="n">v</span><span class="p">),</span> <span class="n">Info</span> <span class="p">(</span><span class="o">-</span><span class="n">vv</span><span class="p">)</span> <span class="ow">and</span>
                      <span class="n">Debug</span><span class="p">(</span><span class="o">-</span><span class="n">vvv</span><span class="p">)</span><span class="o">.</span>

<span class="o">--</span><span class="n">log</span> <span class="n">LOG_FILE</span>        <span class="n">Path</span> <span class="n">to</span> <span class="n">the</span> <span class="n">directory</span> <span class="n">where</span> <span class="n">to</span> <span class="n">store</span> <span class="n">the</span> <span class="s1">&#39;macsyfinder.log&#39;</span>
                      <span class="n">log</span> <span class="n">file</span><span class="o">.</span>

<span class="o">--</span><span class="n">config</span> <span class="n">CFG_FILE</span>     <span class="n">Path</span> <span class="n">to</span> <span class="n">a</span> <span class="n">putative</span> <span class="n">MacSyFinder</span> <span class="n">configuration</span> <span class="n">file</span> <span class="n">to</span> <span class="n">be</span>
                      <span class="n">used</span><span class="o">.</span>

<span class="o">--</span><span class="n">previous</span><span class="o">-</span><span class="n">run</span> <span class="n">PREVIOUS_RUN</span>
                      <span class="n">Path</span> <span class="n">to</span> <span class="n">a</span> <span class="n">previous</span> <span class="n">MacSyFinder</span> <span class="n">run</span> <span class="n">directory</span><span class="o">.</span> <span class="n">It</span> <span class="n">allows</span> <span class="n">to</span>
                      <span class="n">skip</span> <span class="n">the</span> <span class="n">Hmmer</span> <span class="n">search</span> <span class="n">step</span> <span class="n">on</span> <span class="n">same</span> <span class="n">dataset</span><span class="p">,</span> <span class="k">as</span> <span class="n">it</span> <span class="n">uses</span>
                      <span class="n">previous</span> <span class="n">run</span> <span class="n">results</span> <span class="ow">and</span> <span class="n">thus</span> <span class="n">parameters</span> <span class="n">regarding</span>
                      <span class="n">Hmmer</span> <span class="n">detection</span><span class="o">.</span> <span class="n">The</span> <span class="n">configuration</span> <span class="n">file</span> <span class="kn">from</span> <span class="nn">this</span>
                      <span class="n">previous</span> <span class="n">run</span> <span class="n">will</span> <span class="n">be</span> <span class="n">used</span><span class="o">.</span>
                      <span class="n">It</span> <span class="ow">is</span> <span class="ow">in</span> <span class="n">conflict</span> <span class="k">with</span> <span class="n">options</span><span class="p">:</span>
                      <span class="o">--</span><span class="n">config</span><span class="p">,</span>
                      <span class="o">--</span><span class="n">sequence_db</span><span class="p">,</span>
                      <span class="o">--</span><span class="n">profile</span><span class="o">-</span><span class="n">suffix</span><span class="p">,</span>
                      <span class="o">--</span><span class="n">res</span><span class="o">-</span><span class="n">extract</span><span class="o">-</span><span class="n">suffix</span><span class="p">,</span>
                      <span class="o">--</span><span class="n">e</span><span class="o">-</span><span class="n">value</span><span class="o">-</span><span class="n">res</span><span class="p">,</span>
                      <span class="o">--</span><span class="n">db</span><span class="o">-</span><span class="nb">type</span><span class="p">,</span>
                      <span class="o">--</span><span class="n">hmmer</span>
</pre></div>
</div>
</div>
<div class="section" id="configuration-file">
<span id="config-definition-label"></span><h2>Configuration file<a class="headerlink" href="#configuration-file" title="Permalink to this headline"></a></h2>
<p>Options to run MacSyFinder can be specified in a configuration file. The <a class="reference internal" href="config.html#config"><span class="std std-ref">Config</span></a> handles all configuration options for MacSyFinder.
Three locations are parsed to find configuration files:</p>
<blockquote>
<div><ul class="simple">
<li>$PREFIX/etc/macsyfinder/macsyfinder.conf</li>
<li>$(HOME)/.macsyfinder/macsyfinder.conf</li>
<li>./macsyfinder.conf</li>
</ul>
</div></blockquote>
<p>Moreover these three locations options can be passed on the command-line.</p>
<p>Each file can define options, at the end all options are added. If an option is specified several times:</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p>The precedence rules from the less important to the more important are:</p>
<p class="last">$PREFIX/etc/macsyfinder/macsyfinder.conf &lt; $(HOME)/.macsyfinder/macsyfinder.conf &lt; ./macsyfinder.conf &lt; &#8220;command-line&#8221; options</p>
</div>
<p>This means that command-line options will always bypass those from the configuration files. In the same flavor, options altering the definition of systems found in the command-line or the configuration file will always overwhelm values from systems&#8217; <a class="reference internal" href="system_definition.html#system-definition-grammar-label"><span class="std std-ref">XML definition files</span></a>.</p>
<p>The configuration files must follow the Python &#8220;ini&#8221; file syntax.
The Config object provides some default values and performs some validations of the values, for instance:</p>
<p>In MacSyFinder, five sections are defined:</p>
<blockquote>
<div><blockquote id="config-base-label">
<div><ul>
<li><p class="first"><strong>base</strong> : all information related to the protein dataset under study</p>
<ul>
<li><p class="first"><em>file</em> : the path to the dataset in Fasta format (<em>no default value</em>)</p>
</li>
<li><p class="first"><em>type</em> : the type of dataset to handle, four types are supported:</p>
<blockquote>
<div><ul class="simple">
<li><em>unordered</em> : a set of sequences (<em>e.g.</em> a metagenomic dataset)</li>
<li><em>unordered_replicon</em> : a set of sequences corresponding to a complete replicon (<em>e.g.</em> an unassembled complete genome)</li>
<li><em>ordered_replicon</em> : a set of sequences corresponding to a complete replicon ordered (<em>e.g.</em> an assembled complete genome)</li>
<li><em>gembase</em> : a set of multiple ordered replicons.</li>
</ul>
</div></blockquote>
<p>(<em>no default value</em>)</p>
</li>
<li><p class="first"><em>replicon_topology</em> : the topology of the replicon under study. Two topologies are supported: &#8216;linear&#8217; and &#8216;circular&#8217; (<em>default</em> = &#8216;circular&#8217;)
This option will be ignored if the dataset type is not ordered (<em>i.e.</em> &#8220;unordered_replicon&#8221; or &#8220;unordered&#8221;).</p>
</li>
</ul>
</li>
<li><p class="first"><strong>system</strong></p>
<ul class="simple">
<li><em>inter_gene_max_space</em> = list of system name and integer separated by spaces. These values will supersede the values found in the system definition file.</li>
<li><em>min_mandatory_genes_required</em> = list of system name and integer separated by spaces. These values will supersede the values found in the system definition file.</li>
<li><em>min_genes_required</em> = list of system name and integer separated by spaces. These values will supersede the values found in the system definition file.</li>
</ul>
</li>
<li><p class="first"><strong>hmmer</strong></p>
<ul class="simple">
<li><em>hmmer_exe</em> (default= <em>hmmsearch</em> )</li>
<li><em>index_db_exe</em> the executable to use to build the index for the hmm. The value can be &#8216;makeblastdb&#8217; or &#8216;formatdb&#8217; or the absolute path toward one of these two binaries (default= <em>makeblastdb</em> )</li>
<li><em>e_value_res</em> = (default= <em>1</em> )</li>
<li><em>i_evalue_sel</em> = (default= <em>0.5</em> )</li>
<li><em>coverage_profile</em> = (default= <em>0.5</em> )</li>
</ul>
</li>
<li><p class="first"><strong>directories</strong></p>
<ul class="simple">
<li><em>res_search_dir</em> = (default= <em>./datatest/res_search</em> )</li>
<li><em>res_search_suffix</em> = (default= <em>.search_hmm.out</em> )</li>
<li><em>profile_dir</em> = (default= <em>./profiles</em> )</li>
<li><em>profile_suffix</em> = (default= <em>.fasta-aln_edit.hmm</em> )</li>
<li><em>res_extract_suffix</em> = (default= <em>.res_hmm_extract</em> )</li>
<li><em>def_dir</em> = (default= <em>./DEF/</em> )</li>
</ul>
</li>
<li><p class="first"><strong>general</strong></p>
<ul>
<li><dl class="first docutils">
<dt><em>log_level</em>: (default= <em>debug</em> ) This corresponds to an integer code:</dt>
<dd><table border="1" class="first last docutils">
<colgroup>
<col width="38%" />
<col width="62%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Level</th>
<th class="head">Numeric value</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>CRITICAL</td>
<td>50</td>
</tr>
<tr class="row-odd"><td>ERROR</td>
<td>40</td>
</tr>
<tr class="row-even"><td>WARNING</td>
<td>30</td>
</tr>
<tr class="row-odd"><td>INFO</td>
<td>20</td>
</tr>
<tr class="row-even"><td>DEBUG</td>
<td>10</td>
</tr>
<tr class="row-odd"><td>NOTSET</td>
<td>0</td>
</tr>
</tbody>
</table>
</dd>
</dl>
</li>
<li><p class="first"><em>log_file</em> = (default = macsyfinder.log in directory of the run)</p>
</li>
</ul>
</li>
</ul>
</div></blockquote>
</div></blockquote>
<p>Example of a configuration file:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span> <span class="p">[</span><span class="n">base</span><span class="p">]</span>
 <span class="n">prefix</span> <span class="o">=</span> <span class="o">/</span><span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">macsyfinder</span><span class="o">/</span><span class="n">home</span><span class="o">/</span>
 <span class="n">file</span> <span class="o">=</span> <span class="o">%</span><span class="p">(</span><span class="n">prefix</span><span class="p">)</span><span class="n">s</span><span class="o">/</span><span class="n">dataset</span><span class="o">/</span><span class="n">prru_psae</span><span class="o">.</span><span class="mf">001.</span><span class="n">c01</span><span class="o">.</span><span class="n">fasta</span>
 <span class="nb">type</span> <span class="o">=</span> <span class="n">gembase</span>
 <span class="n">replicon_topology</span> <span class="o">=</span> <span class="n">circular</span>

 <span class="p">[</span><span class="n">system</span><span class="p">]</span>
 <span class="n">inter_gene_max_space</span> <span class="o">=</span> <span class="n">T2SS</span> <span class="mi">22</span> <span class="n">Flagellum</span> <span class="mi">44</span>
 <span class="n">min_mandatory_genes_required</span> <span class="o">=</span> <span class="n">T2SS</span> <span class="mi">6</span> <span class="n">Flagellum</span> <span class="mi">4</span>
 <span class="n">min_genes_required</span> <span class="o">=</span> <span class="n">T2SS</span> <span class="mi">8</span> <span class="n">Flagellum</span> <span class="mi">4</span>

 <span class="p">[</span><span class="n">hmmer</span><span class="p">]</span>
 <span class="n">hmmer_exe</span> <span class="o">=</span> <span class="n">hmmsearch</span>
 <span class="n">index_db_exe</span> <span class="o">=</span> <span class="n">makeblastdb</span>
 <span class="n">e_value_res</span> <span class="o">=</span> <span class="mi">1</span>
 <span class="n">i_evalue_sel</span> <span class="o">=</span> <span class="mf">0.5</span>
 <span class="n">coverage_profile</span> <span class="o">=</span> <span class="mf">0.5</span>

 <span class="p">[</span><span class="n">directories</span><span class="p">]</span>
 <span class="n">prefix</span> <span class="o">=</span> <span class="o">/</span><span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">macsyfinder</span><span class="o">/</span><span class="n">home</span><span class="o">/</span>
 <span class="n">def_dir</span> <span class="o">=</span> <span class="o">%</span><span class="p">(</span><span class="n">prefix</span><span class="p">)</span><span class="n">s</span><span class="o">/</span><span class="n">data</span><span class="o">/</span><span class="n">DEF</span>
 <span class="n">res_search_dir</span> <span class="o">=</span> <span class="o">%</span><span class="p">(</span><span class="n">prefix</span><span class="p">)</span><span class="n">s</span><span class="o">/</span><span class="n">dataset</span><span class="o">/</span><span class="n">res_search</span><span class="o">/</span>
 <span class="n">res_search_suffix</span> <span class="o">=</span> <span class="o">.</span><span class="n">raw_hmm</span>
 <span class="n">profile_dir</span> <span class="o">=</span> <span class="o">%</span><span class="p">(</span><span class="n">prefix</span><span class="p">)</span><span class="n">s</span><span class="o">/</span><span class="n">data</span><span class="o">/</span><span class="n">profiles</span>
 <span class="n">profile_suffix</span> <span class="o">=</span> <span class="o">.</span><span class="n">fasta</span><span class="o">-</span><span class="n">aln</span><span class="o">.</span><span class="n">hmm</span>
 <span class="n">res_extract_suffix</span> <span class="o">=</span> <span class="o">.</span><span class="n">res_hmm</span>

<span class="p">[</span><span class="n">general</span><span class="p">]</span>
<span class="n">log_level</span> <span class="o">=</span> <span class="n">debug</span>
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">After a run, the corresponding configuration file (&#8220;macsyfinder.conf&#8221;) is generated as a (re-usable) output file that stores every options used in the run. It is stored in the results&#8217; directory (see <a class="reference internal" href="outputs.html#outputs"><span class="std std-ref">the output section</span></a>).</p>
</div>
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<div class="section" id="in-house-input-files">
<h2>In-house input files<a class="headerlink" href="#in-house-input-files" title="Permalink to this headline"></a></h2>
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<li class="toctree-l1"><a class="reference internal" href="gembase_convention.html">Gembase format</a></li>
<li class="toctree-l1"><a class="reference internal" href="gembase_convention.html#topology-files">Topology files</a></li>
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