<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.Align.Applications._Clustalw</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.Align-module.html">Package Align</a> :: <a href="Bio.Align.Applications-module.html">Package Applications</a> :: Module _Clustalw </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.Align.Applications._Clustalw-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.Align.Applications._Clustalw-module.html" onclick="show_private();">Module Bio.Align.Applications._Clustalw</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2009 by Cymon J. Cox. All rights reserved.</tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">"""Command line wrapper for the multiple alignment program Clustal W.</tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"epytext en"</tt> <tt class="py-comment">#Don't just use plain text in epydoc API pages!</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt> <a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt> <a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Application=Bio.Application-module.html"><a title="Bio.Application" class="py-name" href="#" onclick="return doclink('link-1', 'Application', 'link-1');">Application</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Class Bio.Application._Option=Bio.Application._Option-class.html"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-2', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Class Bio.Application._Switch=Bio.Application._Switch-class.html"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-3', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Class Bio.Application.AbstractCommandline=Bio.Application.AbstractCommandline-class.html"><a title="Bio.Application.AbstractCommandline" class="py-name" href="#" onclick="return doclink('link-4', 'AbstractCommandline', 'link-4');">AbstractCommandline</a></tt> </tt> <a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> </tt> <a name="ClustalwCommandline"></a><div id="ClustalwCommandline-def"><a name="L13"></a><tt class="py-lineno"> 13</tt> <a class="py-toggle" href="#" id="ClustalwCommandline-toggle" onclick="return toggle('ClustalwCommandline');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Align.Applications._Clustalw.ClustalwCommandline-class.html">ClustalwCommandline</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractCommandline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="ClustalwCommandline-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ClustalwCommandline-expanded"><a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> <tt class="py-docstring">"""Command line wrapper for clustalw (version one or two).</tt> </tt> <a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> http://www.clustal.org/</tt> </tt> <a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> Example:</tt> </tt> <a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Align.Applications import ClustalwCommandline</tt> </tt> <a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> >>> in_file = "unaligned.fasta"</tt> </tt> <a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> >>> clustalw_cline = ClustalwCommandline("clustalw2", infile=in_file)</tt> </tt> <a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> >>> print clustalw_cline</tt> </tt> <a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> clustalw2 -infile=unaligned.fasta</tt> </tt> <a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> You would typically run the command line with clustalw_cline() or via</tt> </tt> <a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> the Python subprocess module, as described in the Biopython tutorial.</tt> </tt> <a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> Citation:</tt> </tt> <a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA,</tt> </tt> <a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD,</tt> </tt> <a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0.</tt> </tt> <a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> Bioinformatics, 23, 2947-2948. </tt> </tt> <a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> Last checked against versions: 1.83 and 2.0.10</tt> </tt> <a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Should we default to cmd="clustalw2" now?</tt> </tt> <a name="ClustalwCommandline.__init__"></a><div id="ClustalwCommandline.__init__-def"><a name="L39"></a><tt class="py-lineno"> 39</tt> <a class="py-toggle" href="#" id="ClustalwCommandline.__init__-toggle" onclick="return toggle('ClustalwCommandline.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Applications._Clustalw.ClustalwCommandline-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cmd</tt><tt class="py-op">=</tt><tt class="py-string">"clustalw"</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="ClustalwCommandline.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ClustalwCommandline.__init__-expanded"><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parameters</tt> <tt class="py-op">=</tt> \ </tt> <a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-op">[</tt> </tt> <a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt id="link-5" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-5', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-infile"</tt><tt class="py-op">,</tt> <tt class="py-string">"-INFILE"</tt><tt class="py-op">,</tt> <tt class="py-string">"INFILE"</tt><tt class="py-op">,</tt> <tt class="py-string">"infile"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-string">"Input sequences."</tt><tt class="py-op">,</tt> </tt> <a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-6', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-profile1"</tt><tt class="py-op">,</tt> <tt class="py-string">"-PROFILE1"</tt><tt class="py-op">,</tt> <tt class="py-string">"PROFILE1"</tt><tt class="py-op">,</tt> <tt class="py-string">"profile1"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-string">"Profiles (old alignment)."</tt><tt class="py-op">,</tt> </tt> <a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt id="link-7" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-7', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-profile2"</tt><tt class="py-op">,</tt> <tt class="py-string">"-PROFILE2"</tt><tt class="py-op">,</tt> <tt class="py-string">"PROFILE2"</tt><tt class="py-op">,</tt> <tt class="py-string">"profile2"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-string">"Profiles (old alignment)."</tt><tt class="py-op">,</tt> </tt> <a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-comment">################## VERBS (do things) #############################</tt> </tt> <a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt id="link-8" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-8', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-options"</tt><tt class="py-op">,</tt> <tt class="py-string">"-OPTIONS"</tt><tt class="py-op">,</tt> <tt class="py-string">"OPTIONS"</tt><tt class="py-op">,</tt> <tt class="py-string">"options"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-string">"List the command line parameters"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt id="link-9" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-9', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-help"</tt><tt class="py-op">,</tt> <tt class="py-string">"-HELP"</tt><tt class="py-op">,</tt> <tt class="py-string">"HELP"</tt><tt class="py-op">,</tt> <tt class="py-string">"help"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-string">"Outline the command line params."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt id="link-10" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-10', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-check"</tt><tt class="py-op">,</tt> <tt class="py-string">"-CHECK"</tt><tt class="py-op">,</tt> <tt class="py-string">"CHECK"</tt><tt class="py-op">,</tt> <tt class="py-string">"check"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-string">"Outline the command line params."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt id="link-11" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-11', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-fullhelp"</tt><tt class="py-op">,</tt> <tt class="py-string">"-FULLHELP"</tt><tt class="py-op">,</tt> <tt class="py-string">"FULLHELP"</tt><tt class="py-op">,</tt> <tt class="py-string">"fullhelp"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-string">"Output full help content."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt id="link-12" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-12', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-align"</tt><tt class="py-op">,</tt> <tt class="py-string">"-ALIGN"</tt><tt class="py-op">,</tt> <tt class="py-string">"ALIGN"</tt><tt class="py-op">,</tt> <tt class="py-string">"align"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-string">"Do full multiple alignment."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-13', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-tree"</tt><tt class="py-op">,</tt> <tt class="py-string">"-TREE"</tt><tt class="py-op">,</tt> <tt class="py-string">"TREE"</tt><tt class="py-op">,</tt> <tt class="py-string">"tree"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-string">"Calculate NJ tree."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-14', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-bootstrap"</tt><tt class="py-op">,</tt> <tt class="py-string">"-BOOTSTRAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"BOOTSTRAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"bootstrap"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-string">"Bootstrap a NJ tree (n= number of bootstraps; def. = 1000)."</tt><tt class="py-op">,</tt> </tt> <a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-15" class="py-name" targets="Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-15', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-16', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt id="link-17" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-17', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-convert"</tt><tt class="py-op">,</tt> <tt class="py-string">"-CONVERT"</tt><tt class="py-op">,</tt> <tt class="py-string">"CONVERT"</tt><tt class="py-op">,</tt> <tt class="py-string">"convert"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-string">"Output the input sequences in a different file format."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-comment">##################### PARAMETERS (set things) #########################</tt> </tt> <a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-comment"># ***General settings:****</tt> </tt> <a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-comment"># Makes no sense in biopython</tt> </tt> <a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-comment">#_Option(["-interactive", "-INTERACTIVE", "INTERACTIVE", "interactive"],</tt> </tt> <a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-comment"># [],</tt> </tt> <a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-comment"># lambda x: 0, #Does not take value</tt> </tt> <a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-comment"># False,</tt> </tt> <a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-comment"># "read command line, then enter normal interactive menus",</tt> </tt> <a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-comment"># False),</tt> </tt> <a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt id="link-18" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-18', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-quicktree"</tt><tt class="py-op">,</tt> <tt class="py-string">"-QUICKTREE"</tt><tt class="py-op">,</tt> <tt class="py-string">"QUICKTREE"</tt><tt class="py-op">,</tt> <tt class="py-string">"quicktree"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-string">"Use FAST algorithm for the alignment guide tree"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-19', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-type"</tt><tt class="py-op">,</tt> <tt class="py-string">"-TYPE"</tt><tt class="py-op">,</tt> <tt class="py-string">"TYPE"</tt><tt class="py-op">,</tt> <tt class="py-string">"type"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-string">"PROTEIN or DNA sequences"</tt><tt class="py-op">,</tt> </tt> <a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-20" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-20', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-21" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-21', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"PROTEIN"</tt><tt class="py-op">,</tt> <tt class="py-string">"DNA"</tt><tt class="py-op">,</tt> </tt> <a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-string">"protein"</tt><tt class="py-op">,</tt> <tt class="py-string">"dna"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-22', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-negative"</tt><tt class="py-op">,</tt> <tt class="py-string">"-NEGATIVE"</tt><tt class="py-op">,</tt> <tt class="py-string">"NEGATIVE"</tt><tt class="py-op">,</tt> <tt class="py-string">"negative"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-string">"Protein alignment with negative values in matrix"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt id="link-23" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-23', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-outfile"</tt><tt class="py-op">,</tt> <tt class="py-string">"-OUTFILE"</tt><tt class="py-op">,</tt> <tt class="py-string">"OUTFILE"</tt><tt class="py-op">,</tt> <tt class="py-string">"outfile"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-string">"Output sequence alignment file name"</tt><tt class="py-op">,</tt> </tt> <a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-24', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-output"</tt><tt class="py-op">,</tt> <tt class="py-string">"-OUTPUT"</tt><tt class="py-op">,</tt> <tt class="py-string">"OUTPUT"</tt><tt class="py-op">,</tt> <tt class="py-string">"output"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-string">"Output format: GCG, GDE, PHYLIP, PIR or NEXUS"</tt><tt class="py-op">,</tt> </tt> <a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-25" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-25', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-26" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-26', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"GCG"</tt><tt class="py-op">,</tt> <tt class="py-string">"GDE"</tt><tt class="py-op">,</tt> <tt class="py-string">"PHYLIP"</tt><tt class="py-op">,</tt> </tt> <a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-string">"PIR"</tt><tt class="py-op">,</tt> <tt class="py-string">"NEXUS"</tt><tt class="py-op">,</tt> </tt> <a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-string">"gcg"</tt><tt class="py-op">,</tt> <tt class="py-string">"gde"</tt><tt class="py-op">,</tt> <tt class="py-string">"phylip"</tt><tt class="py-op">,</tt> </tt> <a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-string">"pir"</tt><tt class="py-op">,</tt> <tt class="py-string">"nexus"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt id="link-27" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-27', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-outorder"</tt><tt class="py-op">,</tt> <tt class="py-string">"-OUTORDER"</tt><tt class="py-op">,</tt> <tt class="py-string">"OUTORDER"</tt><tt class="py-op">,</tt> <tt class="py-string">"outorder"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-string">"Output taxon order: INPUT or ALIGNED"</tt><tt class="py-op">,</tt> </tt> <a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-28" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-28', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-29" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-29', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"INPUT"</tt><tt class="py-op">,</tt> <tt class="py-string">"input"</tt><tt class="py-op">,</tt> </tt> <a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-string">"ALIGNED"</tt><tt class="py-op">,</tt> <tt class="py-string">"aligned"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt id="link-30" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-30', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-case"</tt><tt class="py-op">,</tt> <tt class="py-string">"-CASE"</tt><tt class="py-op">,</tt> <tt class="py-string">"CASE"</tt><tt class="py-op">,</tt> <tt class="py-string">"case"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-string">"LOWER or UPPER (for GDE output only)"</tt><tt class="py-op">,</tt> </tt> <a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-31" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-31', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-32" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-32', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"UPPER"</tt><tt class="py-op">,</tt> <tt class="py-string">"upper"</tt><tt class="py-op">,</tt> </tt> <a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-string">"LOWER"</tt><tt class="py-op">,</tt> <tt class="py-string">"lower"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt id="link-33" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-33', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-seqnos"</tt><tt class="py-op">,</tt> <tt class="py-string">"-SEQNOS"</tt><tt class="py-op">,</tt> <tt class="py-string">"SEQNOS"</tt><tt class="py-op">,</tt> <tt class="py-string">"seqnos"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-string">"OFF or ON (for Clustal output only)"</tt><tt class="py-op">,</tt> </tt> <a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-34" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-34', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-35" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-35', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"ON"</tt><tt class="py-op">,</tt> <tt class="py-string">"on"</tt><tt class="py-op">,</tt> </tt> <a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-string">"OFF"</tt><tt class="py-op">,</tt> <tt class="py-string">"off"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt id="link-36" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-36', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-seqno_range"</tt><tt class="py-op">,</tt> <tt class="py-string">"-SEQNO_RANGE"</tt><tt class="py-op">,</tt> <tt class="py-string">"SEQNO_RANGE"</tt><tt class="py-op">,</tt> <tt class="py-string">"seqno_range"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-string">"OFF or ON (NEW- for all output formats)"</tt><tt class="py-op">,</tt> </tt> <a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-37" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-37', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-38" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-38', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"ON"</tt><tt class="py-op">,</tt> <tt class="py-string">"on"</tt><tt class="py-op">,</tt> </tt> <a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-string">"OFF"</tt><tt class="py-op">,</tt> <tt class="py-string">"off"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt id="link-39" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-39', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-range"</tt><tt class="py-op">,</tt> <tt class="py-string">"-RANGE"</tt><tt class="py-op">,</tt> <tt class="py-string">"RANGE"</tt><tt class="py-op">,</tt> <tt class="py-string">"range"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-string">"Sequence range to write starting m to m+n. "</tt> </tt> <a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-string">"Input as string eg. '24,200'"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt id="link-40" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-40', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-maxseqlen"</tt><tt class="py-op">,</tt> <tt class="py-string">"-MAXSEQLEN"</tt><tt class="py-op">,</tt> <tt class="py-string">"MAXSEQLEN"</tt><tt class="py-op">,</tt> <tt class="py-string">"maxseqlen"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-string">"Maximum allowed input sequence length"</tt><tt class="py-op">,</tt> </tt> <a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-41" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-41', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-42" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-42', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-43', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-quiet"</tt><tt class="py-op">,</tt> <tt class="py-string">"-QUIET"</tt><tt class="py-op">,</tt> <tt class="py-string">"QUIET"</tt><tt class="py-op">,</tt> <tt class="py-string">"quiet"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-string">"Reduce console output to minimum"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt id="link-44" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-44', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-stats"</tt><tt class="py-op">,</tt> <tt class="py-string">"-STATS"</tt><tt class="py-op">,</tt> <tt class="py-string">"STATS"</tt><tt class="py-op">,</tt> <tt class="py-string">"stats"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-string">"Log some alignents statistics to file"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-comment"># ***Fast Pairwise Alignments:***</tt> </tt> <a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt id="link-45" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-45', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-ktuple"</tt><tt class="py-op">,</tt> <tt class="py-string">"-KTUPLE"</tt><tt class="py-op">,</tt> <tt class="py-string">"KTUPLE"</tt><tt class="py-op">,</tt> <tt class="py-string">"ktuple"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-string">"Word size"</tt><tt class="py-op">,</tt> </tt> <a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-46" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-46', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-47" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-47', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-48" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-48', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt id="link-49" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-49', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-topdiags"</tt><tt class="py-op">,</tt> <tt class="py-string">"-TOPDIAGS"</tt><tt class="py-op">,</tt> <tt class="py-string">"TOPDIAGS"</tt><tt class="py-op">,</tt> <tt class="py-string">"topdiags"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-string">"Number of best diags."</tt><tt class="py-op">,</tt> </tt> <a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-50" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-50', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-51" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-51', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-52" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-52', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt id="link-53" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-53', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-window"</tt><tt class="py-op">,</tt> <tt class="py-string">"-WINDOW"</tt><tt class="py-op">,</tt> <tt class="py-string">"WINDOW"</tt><tt class="py-op">,</tt> <tt class="py-string">"window"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-string">"Window around best diags."</tt><tt class="py-op">,</tt> </tt> <a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-54" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-54', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-55" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-55', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-56" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-56', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt id="link-57" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-57', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-pairgap"</tt><tt class="py-op">,</tt> <tt class="py-string">"-PAIRGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"PAIRGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"pairgap"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-string">"Gap penalty"</tt><tt class="py-op">,</tt> </tt> <a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-58" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-58', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-59" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-59', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-60" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-60', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt id="link-61" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-61', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-score"</tt><tt class="py-op">,</tt> <tt class="py-string">"-SCORE"</tt><tt class="py-op">,</tt> <tt class="py-string">"SCORE"</tt><tt class="py-op">,</tt> <tt class="py-string">"score"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-string">"Either: PERCENT or ABSOLUTE"</tt><tt class="py-op">,</tt> </tt> <a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-62" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-62', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-63" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-63', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"percent"</tt><tt class="py-op">,</tt> <tt class="py-string">"PERCENT"</tt><tt class="py-op">,</tt> </tt> <a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-string">"absolute"</tt><tt class="py-op">,</tt><tt class="py-string">"ABSOLUTE"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-comment"># ***Slow Pairwise Alignments:***</tt> </tt> <a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt id="link-64" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-64', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-pwmatrix"</tt><tt class="py-op">,</tt> <tt class="py-string">"-PWMATRIX"</tt><tt class="py-op">,</tt> <tt class="py-string">"PWMATRIX"</tt><tt class="py-op">,</tt> <tt class="py-string">"pwmatrix"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-string">"Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename"</tt><tt class="py-op">,</tt> </tt> <a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-65" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-65', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-66" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-66', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"BLOSUM"</tt><tt class="py-op">,</tt> <tt class="py-string">"PAM"</tt><tt class="py-op">,</tt> </tt> <a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-string">"GONNET"</tt><tt class="py-op">,</tt> <tt class="py-string">"ID"</tt><tt class="py-op">,</tt> </tt> <a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-string">"blosum"</tt><tt class="py-op">,</tt> <tt class="py-string">"pam"</tt><tt class="py-op">,</tt> </tt> <a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-string">"gonnet"</tt><tt class="py-op">,</tt> <tt class="py-string">"id"</tt><tt class="py-op">]</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-67', 'x', 'link-15');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt id="link-68" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-68', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-pwdnamatrix"</tt><tt class="py-op">,</tt> <tt class="py-string">"-PWDNAMATRIX"</tt><tt class="py-op">,</tt> <tt class="py-string">"PWDNAMATRIX"</tt><tt class="py-op">,</tt> <tt class="py-string">"pwdnamatrix"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-string">"DNA weight matrix=IUB, CLUSTALW or filename"</tt><tt class="py-op">,</tt> </tt> <a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-69" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-69', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-70" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-70', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"IUB"</tt><tt class="py-op">,</tt> <tt class="py-string">"CLUSTALW"</tt><tt class="py-op">,</tt> </tt> <a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-string">"iub"</tt><tt class="py-op">,</tt> <tt class="py-string">"clustalw"</tt><tt class="py-op">]</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt id="link-71" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-71', 'x', 'link-15');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt id="link-72" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-72', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-pwgapopen"</tt><tt class="py-op">,</tt> <tt class="py-string">"-PWGAPOPEN"</tt><tt class="py-op">,</tt> <tt class="py-string">"PWGAPOPEN"</tt><tt class="py-op">,</tt> <tt class="py-string">"pwgapopen"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-string">"Gap opening penalty"</tt><tt class="py-op">,</tt> </tt> <a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-73" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-73', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-74" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-74', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-75', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt id="link-76" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-76', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-pwgapext"</tt><tt class="py-op">,</tt> <tt class="py-string">"-PWGAPEXT"</tt><tt class="py-op">,</tt> <tt class="py-string">"PWGAPEXT"</tt><tt class="py-op">,</tt> <tt class="py-string">"pwgapext"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-string">"Gap opening penalty"</tt><tt class="py-op">,</tt> </tt> <a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-77" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-77', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-78', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-79', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-comment"># ***Multiple Alignments:***</tt> </tt> <a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt id="link-80" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-80', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-newtree"</tt><tt class="py-op">,</tt> <tt class="py-string">"-NEWTREE"</tt><tt class="py-op">,</tt> <tt class="py-string">"NEWTREE"</tt><tt class="py-op">,</tt> <tt class="py-string">"newtree"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-string">"Output file name for newly created guide tree"</tt><tt class="py-op">,</tt> </tt> <a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt id="link-81" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-81', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-usetree"</tt><tt class="py-op">,</tt> <tt class="py-string">"-USETREE"</tt><tt class="py-op">,</tt> <tt class="py-string">"USETREE"</tt><tt class="py-op">,</tt> <tt class="py-string">"usetree"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-string">"File name of guide tree"</tt><tt class="py-op">,</tt> </tt> <a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-82" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-82', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">,</tt> </tt> <a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt id="link-83" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-83', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-matrix"</tt><tt class="py-op">,</tt> <tt class="py-string">"-MATRIX"</tt><tt class="py-op">,</tt> <tt class="py-string">"MATRIX"</tt><tt class="py-op">,</tt> <tt class="py-string">"matrix"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-string">"Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename"</tt><tt class="py-op">,</tt> </tt> <a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-84" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-84', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-85" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-85', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"BLOSUM"</tt><tt class="py-op">,</tt> <tt class="py-string">"PAM"</tt><tt class="py-op">,</tt> </tt> <a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-string">"GONNET"</tt><tt class="py-op">,</tt> <tt class="py-string">"ID"</tt><tt class="py-op">,</tt> </tt> <a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-string">"blosum"</tt><tt class="py-op">,</tt> <tt class="py-string">"pam"</tt><tt class="py-op">,</tt> </tt> <a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-string">"gonnet"</tt><tt class="py-op">,</tt> <tt class="py-string">"id"</tt><tt class="py-op">]</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt id="link-86" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-86', 'x', 'link-15');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt id="link-87" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-87', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-dnamatrix"</tt><tt class="py-op">,</tt> <tt class="py-string">"-DNAMATRIX"</tt><tt class="py-op">,</tt> <tt class="py-string">"DNAMATRIX"</tt><tt class="py-op">,</tt> <tt class="py-string">"dnamatrix"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-string">"DNA weight matrix=IUB, CLUSTALW or filename"</tt><tt class="py-op">,</tt> </tt> <a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-88" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-88', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-89" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-89', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"IUB"</tt><tt class="py-op">,</tt> <tt class="py-string">"CLUSTALW"</tt><tt class="py-op">,</tt> </tt> <a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-string">"iub"</tt><tt class="py-op">,</tt> <tt class="py-string">"clustalw"</tt><tt class="py-op">]</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">(</tt><tt id="link-90" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-90', 'x', 'link-15');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt id="link-91" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-91', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-gapopen"</tt><tt class="py-op">,</tt> <tt class="py-string">"-GAPOPEN"</tt><tt class="py-op">,</tt> <tt class="py-string">"GAPOPEN"</tt><tt class="py-op">,</tt> <tt class="py-string">"gapopen"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-string">"Gap opening penalty"</tt><tt class="py-op">,</tt> </tt> <a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-92" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-92', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-93" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-93', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-94" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-94', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt id="link-95" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-95', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-gapext"</tt><tt class="py-op">,</tt> <tt class="py-string">"-GAPEXT"</tt><tt class="py-op">,</tt> <tt class="py-string">"GAPEXT"</tt><tt class="py-op">,</tt> <tt class="py-string">"gapext"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-string">"Gap extension penalty"</tt><tt class="py-op">,</tt> </tt> <a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-96" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-96', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-97" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-97', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-98" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-98', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt id="link-99" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-99', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-endgaps"</tt><tt class="py-op">,</tt> <tt class="py-string">"-ENDGAPS"</tt><tt class="py-op">,</tt> <tt class="py-string">"ENDGAPS"</tt><tt class="py-op">,</tt> <tt class="py-string">"endgaps"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-string">"No end gap separation pen."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt id="link-100" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-100', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-gapdist"</tt><tt class="py-op">,</tt> <tt class="py-string">"-GAPDIST"</tt><tt class="py-op">,</tt> <tt class="py-string">"GAPDIST"</tt><tt class="py-op">,</tt> <tt class="py-string">"gapdist"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-string">"Gap separation pen. range"</tt><tt class="py-op">,</tt> </tt> <a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-101" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-101', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-102" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-102', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-103" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-103', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt id="link-104" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-104', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-nopgap"</tt><tt class="py-op">,</tt> <tt class="py-string">"-NOPGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"NOPGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"nopgap"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-string">"Residue-specific gaps off"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt id="link-105" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-105', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-nohgap"</tt><tt class="py-op">,</tt> <tt class="py-string">"-NOHGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"NOHGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"nohgap"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-string">"Hydrophilic gaps off"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt id="link-106" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-106', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-hgapresidues"</tt><tt class="py-op">,</tt> <tt class="py-string">"-HGAPRESIDUES"</tt><tt class="py-op">,</tt> <tt class="py-string">"HGAPRESIDUES"</tt><tt class="py-op">,</tt> <tt class="py-string">"hgapresidues"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-string">"List hydrophilic res."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt id="link-107" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-107', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-maxdiv"</tt><tt class="py-op">,</tt> <tt class="py-string">"-MAXDIV"</tt><tt class="py-op">,</tt> <tt class="py-string">"MAXDIV"</tt><tt class="py-op">,</tt> <tt class="py-string">"maxdiv"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-string">"% ident. for delay"</tt><tt class="py-op">,</tt> </tt> <a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-108" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-108', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-109" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-109', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-110" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-110', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt id="link-111" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-111', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-transweight"</tt><tt class="py-op">,</tt> <tt class="py-string">"-TRANSWEIGHT"</tt><tt class="py-op">,</tt> <tt class="py-string">"TRANSWEIGHT"</tt><tt class="py-op">,</tt> <tt class="py-string">"transweight"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-string">"Transitions weighting"</tt><tt class="py-op">,</tt> </tt> <a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-112" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-112', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-113" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-113', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-114" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-114', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt id="link-115" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-115', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-iteration"</tt><tt class="py-op">,</tt> <tt class="py-string">"-ITERATION"</tt><tt class="py-op">,</tt> <tt class="py-string">"ITERATION"</tt><tt class="py-op">,</tt> <tt class="py-string">"iteration"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-string">"NONE or TREE or ALIGNMENT"</tt><tt class="py-op">,</tt> </tt> <a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-116" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-116', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-117" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-117', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"NONE"</tt><tt class="py-op">,</tt> <tt class="py-string">"TREE"</tt><tt class="py-op">,</tt> </tt> <a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-string">"ALIGNMENT"</tt><tt class="py-op">,</tt> </tt> <a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-string">"none"</tt><tt class="py-op">,</tt> <tt class="py-string">"tree"</tt><tt class="py-op">,</tt> </tt> <a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-string">"alignment"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt id="link-118" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-118', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-numiter"</tt><tt class="py-op">,</tt> <tt class="py-string">"-NUMITER"</tt><tt class="py-op">,</tt> <tt class="py-string">"NUMITER"</tt><tt class="py-op">,</tt> <tt class="py-string">"numiter"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-string">"maximum number of iterations to perform"</tt><tt class="py-op">,</tt> </tt> <a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-119" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-119', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-120" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-120', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt id="link-121" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-121', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-noweights"</tt><tt class="py-op">,</tt> <tt class="py-string">"-NOWEIGHTS"</tt><tt class="py-op">,</tt> <tt class="py-string">"NOWEIGHTS"</tt><tt class="py-op">,</tt> <tt class="py-string">"noweights"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-string">"Disable sequence weighting"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-comment"># ***Profile Alignments:***</tt> </tt> <a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt id="link-122" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-122', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-profile"</tt><tt class="py-op">,</tt> <tt class="py-string">"-PROFILE"</tt><tt class="py-op">,</tt> <tt class="py-string">"PROFILE"</tt><tt class="py-op">,</tt> <tt class="py-string">"profile"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-string">"Merge two alignments by profile alignment"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt id="link-123" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-123', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-newtree1"</tt><tt class="py-op">,</tt> <tt class="py-string">"-NEWTREE1"</tt><tt class="py-op">,</tt> <tt class="py-string">"NEWTREE1"</tt><tt class="py-op">,</tt> <tt class="py-string">"newtree1"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-string">"Output file name for new guide tree of profile1"</tt><tt class="py-op">,</tt> </tt> <a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt id="link-124" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-124', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-newtree2"</tt><tt class="py-op">,</tt> <tt class="py-string">"-NEWTREE2"</tt><tt class="py-op">,</tt> <tt class="py-string">"NEWTREE2"</tt><tt class="py-op">,</tt> <tt class="py-string">"newtree2"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-string">"Output file for new guide tree of profile2"</tt><tt class="py-op">,</tt> </tt> <a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt id="link-125" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-125', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-usetree1"</tt><tt class="py-op">,</tt> <tt class="py-string">"-USETREE1"</tt><tt class="py-op">,</tt> <tt class="py-string">"USETREE1"</tt><tt class="py-op">,</tt> <tt class="py-string">"usetree1"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-string">"File name of guide tree for profile1"</tt><tt class="py-op">,</tt> </tt> <a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-126" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-126', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">,</tt> </tt> <a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt id="link-127" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-127', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-usetree2"</tt><tt class="py-op">,</tt> <tt class="py-string">"-USETREE2"</tt><tt class="py-op">,</tt> <tt class="py-string">"USETREE2"</tt><tt class="py-op">,</tt> <tt class="py-string">"usetree2"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-string">"File name of guide tree for profile2"</tt><tt class="py-op">,</tt> </tt> <a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-128" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-128', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">exists</tt><tt class="py-op">,</tt> </tt> <a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-comment"># ***Sequence to Profile Alignments:***</tt> </tt> <a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt id="link-129" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-129', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-sequences"</tt><tt class="py-op">,</tt> <tt class="py-string">"-SEQUENCES"</tt><tt class="py-op">,</tt> <tt class="py-string">"SEQUENCES"</tt><tt class="py-op">,</tt> <tt class="py-string">"sequences"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-string">"Sequentially add profile2 sequences to profile1 alignment"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt id="link-130" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-130', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-nosecstr1"</tt><tt class="py-op">,</tt> <tt class="py-string">"-NOSECSTR1"</tt><tt class="py-op">,</tt> <tt class="py-string">"NOSECSTR1"</tt><tt class="py-op">,</tt> <tt class="py-string">"nosecstr1"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-string">"Do not use secondary structure-gap penalty mask for profile 1"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt id="link-131" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-131', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-nosecstr2"</tt><tt class="py-op">,</tt> <tt class="py-string">"-NOSECSTR2"</tt><tt class="py-op">,</tt> <tt class="py-string">"NOSECSTR2"</tt><tt class="py-op">,</tt> <tt class="py-string">"nosecstr2"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-string">"Do not use secondary structure-gap penalty mask for profile 2"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-comment"># ***Structure Alignments:***</tt> </tt> <a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt id="link-132" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-132', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-secstrout"</tt><tt class="py-op">,</tt> <tt class="py-string">"-SECSTROUT"</tt><tt class="py-op">,</tt> <tt class="py-string">"SECSTROUT"</tt><tt class="py-op">,</tt> <tt class="py-string">"secstrout"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-string">"STRUCTURE or MASK or BOTH or NONE output in alignment file"</tt><tt class="py-op">,</tt> </tt> <a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-133" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-133', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-134" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-134', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"STRUCTURE"</tt><tt class="py-op">,</tt> <tt class="py-string">"MASK"</tt><tt class="py-op">,</tt> </tt> <a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-string">"BOTH"</tt><tt class="py-op">,</tt> <tt class="py-string">"NONE"</tt><tt class="py-op">,</tt> </tt> <a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-string">"structure"</tt><tt class="py-op">,</tt> <tt class="py-string">"mask"</tt><tt class="py-op">,</tt> </tt> <a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-string">"both"</tt><tt class="py-op">,</tt> <tt class="py-string">"none"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt id="link-135" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-135', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-helixgap"</tt><tt class="py-op">,</tt> <tt class="py-string">"-HELIXGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"HELIXGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"helixgap"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-string">"Gap penalty for helix core residues"</tt><tt class="py-op">,</tt> </tt> <a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-136" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-136', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-137" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-137', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-138" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-138', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt id="link-139" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-139', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-strandgap"</tt><tt class="py-op">,</tt> <tt class="py-string">"-STRANDGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"STRANDGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"strandgap"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-string">"gap penalty for strand core residues"</tt><tt class="py-op">,</tt> </tt> <a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-140" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-140', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-141" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-141', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-142" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-142', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt id="link-143" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-143', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-loopgap"</tt><tt class="py-op">,</tt> <tt class="py-string">"-LOOPGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"LOOPGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"loopgap"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-string">"Gap penalty for loop regions"</tt><tt class="py-op">,</tt> </tt> <a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-144" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-144', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-145" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-145', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-146" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-146', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt id="link-147" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-147', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-terminalgap"</tt><tt class="py-op">,</tt> <tt class="py-string">"-TERMINALGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"TERMINALGAP"</tt><tt class="py-op">,</tt> <tt class="py-string">"terminalgap"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-string">"Gap penalty for structure termini"</tt><tt class="py-op">,</tt> </tt> <a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-148" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-148', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-149" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-149', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt> <a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-150" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-150', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt id="link-151" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-151', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-helixendin"</tt><tt class="py-op">,</tt> <tt class="py-string">"-HELIXENDIN"</tt><tt class="py-op">,</tt> <tt class="py-string">"HELIXENDIN"</tt><tt class="py-op">,</tt> <tt class="py-string">"helixendin"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-string">"Number of residues inside helix to be treated as terminal"</tt><tt class="py-op">,</tt> </tt> <a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-152" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-152', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-153" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-153', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt id="link-154" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-154', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-helixendout"</tt><tt class="py-op">,</tt> <tt class="py-string">"-HELIXENDOUT"</tt><tt class="py-op">,</tt> <tt class="py-string">"HELIXENDOUT"</tt><tt class="py-op">,</tt> <tt class="py-string">"helixendout"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-string">"Number of residues outside helix to be treated as terminal"</tt><tt class="py-op">,</tt> </tt> <a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-155" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-155', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-156" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-156', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt id="link-157" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-157', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-strandendin"</tt><tt class="py-op">,</tt> <tt class="py-string">"-STRANDENDIN"</tt><tt class="py-op">,</tt> <tt class="py-string">"STRANDENDIN"</tt><tt class="py-op">,</tt> <tt class="py-string">"strandendin"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-string">"Number of residues inside strand to be treated as terminal"</tt><tt class="py-op">,</tt> </tt> <a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-158" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-158', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-159" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-159', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt id="link-160" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-160', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-strandendout"</tt><tt class="py-op">,</tt> <tt class="py-string">"-STRANDENDOUT"</tt><tt class="py-op">,</tt> <tt class="py-string">"STRANDENDOUT"</tt><tt class="py-op">,</tt> <tt class="py-string">"strandendout"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-string">"number of residues outside strand to be treated as terminal"</tt><tt class="py-op">,</tt> </tt> <a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-161" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-161', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-162" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-162', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-comment"># ***Trees:***</tt> </tt> <a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt id="link-163" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-163', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-outputtree"</tt><tt class="py-op">,</tt> <tt class="py-string">"-OUTPUTTREE"</tt><tt class="py-op">,</tt> <tt class="py-string">"OUTPUTTREE"</tt><tt class="py-op">,</tt> <tt class="py-string">"outputtree"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-string">"nj OR phylip OR dist OR nexus"</tt><tt class="py-op">,</tt> </tt> <a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-164" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-164', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-165" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-165', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"NJ"</tt><tt class="py-op">,</tt> <tt class="py-string">"PHYLIP"</tt><tt class="py-op">,</tt> </tt> <a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-string">"DIST"</tt><tt class="py-op">,</tt> <tt class="py-string">"NEXUS"</tt><tt class="py-op">,</tt> </tt> <a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-string">"nj"</tt><tt class="py-op">,</tt> <tt class="py-string">"phylip"</tt><tt class="py-op">,</tt> </tt> <a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-string">"dist"</tt><tt class="py-op">,</tt> <tt class="py-string">"nexus"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt id="link-166" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-166', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-seed"</tt><tt class="py-op">,</tt> <tt class="py-string">"-SEED"</tt><tt class="py-op">,</tt> <tt class="py-string">"SEED"</tt><tt class="py-op">,</tt> <tt class="py-string">"seed"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-string">"Seed number for bootstraps."</tt><tt class="py-op">,</tt> </tt> <a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-167" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-167', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-168" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-168', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt id="link-169" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-169', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-kimura"</tt><tt class="py-op">,</tt> <tt class="py-string">"-KIMURA"</tt><tt class="py-op">,</tt> <tt class="py-string">"KIMURA"</tt><tt class="py-op">,</tt> <tt class="py-string">"kimura"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-string">"Use Kimura's correction."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt id="link-170" class="py-name"><a title="Bio.Application._Switch" class="py-name" href="#" onclick="return doclink('link-170', '_Switch', 'link-3');">_Switch</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-tossgaps"</tt><tt class="py-op">,</tt> <tt class="py-string">"-TOSSGAPS"</tt><tt class="py-op">,</tt> <tt class="py-string">"TOSSGAPS"</tt><tt class="py-op">,</tt> <tt class="py-string">"tossgaps"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-string">"Ignore positions with gaps."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt id="link-171" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-171', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-bootlabels"</tt><tt class="py-op">,</tt> <tt class="py-string">"-BOOTLABELS"</tt><tt class="py-op">,</tt> <tt class="py-string">"BOOTLABELS"</tt><tt class="py-op">,</tt> <tt class="py-string">"bootlabels"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-string">"Node OR branch position of bootstrap values in tree display"</tt><tt class="py-op">,</tt> </tt> <a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-172" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-172', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-173" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-173', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"NODE"</tt><tt class="py-op">,</tt> <tt class="py-string">"BRANCH"</tt><tt class="py-op">,</tt> </tt> <a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-string">"node"</tt><tt class="py-op">,</tt> <tt class="py-string">"branch"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt id="link-174" class="py-name"><a title="Bio.Application._Option" class="py-name" href="#" onclick="return doclink('link-174', '_Option', 'link-2');">_Option</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"-clustering"</tt><tt class="py-op">,</tt> <tt class="py-string">"-CLUSTERING"</tt><tt class="py-op">,</tt> <tt class="py-string">"CLUSTERING"</tt><tt class="py-op">,</tt> <tt class="py-string">"clustering"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-string">"NJ or UPGMA"</tt><tt class="py-op">,</tt> </tt> <a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">checker_function</tt><tt class="py-op">=</tt><tt class="py-keyword">lambda</tt> <tt id="link-175" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-175', 'x', 'link-15');">x</a></tt><tt class="py-op">:</tt> <tt id="link-176" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-176', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"NJ"</tt><tt class="py-op">,</tt> <tt class="py-string">"UPGMA"</tt><tt class="py-op">,</tt> <tt class="py-string">"nj"</tt><tt class="py-op">,</tt> <tt class="py-string">"upgma"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-op">]</tt> </tt> <a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt id="link-177" class="py-name"><a title="Bio.Application.AbstractCommandline" class="py-name" href="#" onclick="return doclink('link-177', 'AbstractCommandline', 'link-4');">AbstractCommandline</a></tt><tt class="py-op">.</tt><tt id="link-178" class="py-name" targets="Method 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Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__ Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__ Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__ Bio.Restriction._Update.Update.ConnectionError.__init__ Bio.Restriction._Update.Update.FtpNameError.__init__ Bio.Restriction._Update.Update.FtpPasswordError.__init__ Bio.Restriction._Update.Update.RebaseUpdate.__init__ Bio.SCOP.Astral.__init__ Bio.SCOP.Cla.Index.__init__ Bio.SCOP.Cla.Record.__init__ Bio.SCOP.Des.Record.__init__ Bio.SCOP.Dom.Record.__init__ Bio.SCOP.Domain.__init__ Bio.SCOP.Hie.Record.__init__ Bio.SCOP.Node.__init__ Bio.SCOP.Raf.Res.__init__ Bio.SCOP.Raf.SeqMap.__init__ Bio.SCOP.Raf.SeqMapIndex.__init__ Bio.SCOP.Residues'.Residues.__init__ Bio.SCOP.Scop.__init__ Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__ Bio.Search.Algorithm.__init__ Bio.Search.Database.__init__ Bio.Search.HSP.__init__ Bio.Search.HSPSeq.__init__ Bio.Search.Hit.__init__ 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Bio.Wise.psw.ColumnUnit.__init__ Bio.kNN.kNN.__init__ Bio.pairwise2.affine_penalty.__init__ Bio.pairwise2.dictionary_match.__init__ Bio.pairwise2.identity_match.__init__ BioSQL.BioSeq.DBSeq.__init__ BioSQL.BioSeq.DBSeqRecord.__init__ BioSQL.BioSeqDatabase.Adaptor.__init__ BioSQL.BioSeqDatabase.BioSeqDatabase.__init__ BioSQL.BioSeqDatabase.DBServer.__init__ BioSQL.DBUtils.Generic_dbutils.__init__ BioSQL.Loader.DatabaseLoader.__init__ BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-178', '__init__', 'link-178');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">cmd</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> </tt> </div></div><a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> </tt> <a name="_test"></a><div id="_test-def"><a name="L309"></a><tt class="py-lineno">309</tt> <a class="py-toggle" href="#" id="_test-toggle" onclick="return toggle('_test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Applications._Clustalw-module.html#_test">_test</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_test-expanded"><a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-docstring">"""Run the module's doctests (PRIVATE)."""</tt> </tt> <a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Runing ClustalW doctests..."</tt> </tt> <a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">doctest</tt> </tt> <a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-name">doctest</tt><tt class="py-op">.</tt><tt class="py-name">testmod</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt> </div><a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> </tt> <a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt> <a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt id="link-179" class="py-name" targets="Function Bio.Align.Applications._Clustalw._test()=Bio.Align.Applications._Clustalw-module.html#_test,Function Bio.Align.Applications._Dialign._test()=Bio.Align.Applications._Dialign-module.html#_test,Function Bio.Align.Applications._Mafft._test()=Bio.Align.Applications._Mafft-module.html#_test,Function Bio.Align.Applications._Muscle._test()=Bio.Align.Applications._Muscle-module.html#_test,Function Bio.Align.Applications._Prank._test()=Bio.Align.Applications._Prank-module.html#_test,Function Bio.Align.Applications._Probcons._test()=Bio.Align.Applications._Probcons-module.html#_test,Function Bio.Align.Applications._TCoffee._test()=Bio.Align.Applications._TCoffee-module.html#_test,Function Bio.Align.Generic._test()=Bio.Align.Generic-module.html#_test,Function Bio.Align._test()=Bio.Align-module.html#_test,Function Bio.AlignIO.StockholmIO._test()=Bio.AlignIO.StockholmIO-module.html#_test,Function Bio.AlignIO._test()=Bio.AlignIO-module.html#_test,Function Bio.Application._test()=Bio.Application-module.html#_test,Function Bio.Blast.Applications._test()=Bio.Blast.Applications-module.html#_test,Function Bio.DocSQL._test()=Bio.DocSQL-module.html#_test,Function Bio.Emboss.Applications._test()=Bio.Emboss.Applications-module.html#_test,Function Bio.KEGG.Compound._test()=Bio.KEGG.Compound-module.html#_test,Function Bio.KEGG.Enzyme._test()=Bio.KEGG.Enzyme-module.html#_test,Function Bio.Motif._test()=Bio.Motif-module.html#_test,Function Bio.PDB.Selection._test()=Bio.PDB.Selection-module.html#_test,Function Bio.Seq._test()=Bio.Seq-module.html#_test,Function Bio.SeqFeature._test()=Bio.SeqFeature-module.html#_test,Function Bio.SeqIO.AceIO._test()=Bio.SeqIO.AceIO-module.html#_test,Function Bio.SeqIO.PhdIO._test()=Bio.SeqIO.PhdIO-module.html#_test,Function Bio.SeqIO.QualityIO._test()=Bio.SeqIO.QualityIO-module.html#_test,Function Bio.SeqIO._test()=Bio.SeqIO-module.html#_test,Function Bio.SeqRecord._test()=Bio.SeqRecord-module.html#_test,Function Bio.SeqUtils._test()=Bio.SeqUtils-module.html#_test,Function Bio.Sequencing.Applications._Novoalign._test()=Bio.Sequencing.Applications._Novoalign-module.html#_test,Function Bio.Statistics.lowess._test()=Bio.Statistics.lowess-module.html#_test,Function Bio.Wise._test()=Bio.Wise-module.html#_test,Function Bio.Wise.dnal._test()=Bio.Wise.dnal-module.html#_test,Function Bio.Wise.psw._test()=Bio.Wise.psw-module.html#_test"><a title="Bio.Align.Applications._Clustalw._test Bio.Align.Applications._Dialign._test Bio.Align.Applications._Mafft._test Bio.Align.Applications._Muscle._test Bio.Align.Applications._Prank._test Bio.Align.Applications._Probcons._test Bio.Align.Applications._TCoffee._test Bio.Align.Generic._test Bio.Align._test Bio.AlignIO.StockholmIO._test Bio.AlignIO._test Bio.Application._test Bio.Blast.Applications._test Bio.DocSQL._test Bio.Emboss.Applications._test Bio.KEGG.Compound._test Bio.KEGG.Enzyme._test Bio.Motif._test Bio.PDB.Selection._test Bio.Seq._test Bio.SeqFeature._test Bio.SeqIO.AceIO._test Bio.SeqIO.PhdIO._test Bio.SeqIO.QualityIO._test Bio.SeqIO._test Bio.SeqRecord._test Bio.SeqUtils._test Bio.Sequencing.Applications._Novoalign._test Bio.Statistics.lowess._test Bio.Wise._test Bio.Wise.dnal._test Bio.Wise.psw._test" class="py-name" href="#" onclick="return doclink('link-179', '_test', 'link-179');">_test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> </tt><script type="text/javascript"> <!-- expandto(location.href); // --> </script> </pre> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Thu Aug 18 18:22:44 2011 </td> <td align="right" class="footer"> <a target="mainFrame" 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