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_modules/index.html

@@ -30,12 +30,9 @@
           <div class="body" role="main">
 
   <h1>All modules for which code is available</h1>
-<ul><li><a href="seguid/asserts.html">seguid.asserts</a></li>
-<li><a href="seguid/chksum.html">seguid.chksum</a></li>
+<ul><li><a href="seguid/chksum.html">seguid.chksum</a></li>
 <li><a href="seguid/config.html">seguid.config</a></li>
-<li><a href="seguid/manip.html">seguid.manip</a></li>
 <li><a href="seguid/reprutils.html">seguid.reprutils</a></li>
-<li><a href="seguid/tables.html">seguid.tables</a></li>
 </ul>
 
           </div>

_modules/seguid/chksum.html

@@ -53,13 +53,13 @@ <h1>Source code for seguid.chksum</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">hashlib</span>
 <span class="kn">import</span> <span class="nn">base64</span>
 
-<span class="kn">from</span> <span class="nn">seguid.manip</span> <span class="kn">import</span> <span class="n">reverse</span>
-<span class="kn">from</span> <span class="nn">seguid.manip</span> <span class="kn">import</span> <span class="n">rotate</span>
-<span class="kn">from</span> <span class="nn">seguid.manip</span> <span class="kn">import</span> <span class="n">rotate_to_min</span>
+<span class="kn">from</span> <span class="nn">seguid._manip</span> <span class="kn">import</span> <span class="n">reverse</span>
+<span class="kn">from</span> <span class="nn">seguid._manip</span> <span class="kn">import</span> <span class="n">rotate</span>
+<span class="kn">from</span> <span class="nn">seguid._manip</span> <span class="kn">import</span> <span class="n">rotate_to_min</span>
 
-<span class="kn">from</span> <span class="nn">seguid.tables</span> <span class="kn">import</span> <span class="n">tablefactory</span>
-<span class="kn">from</span> <span class="nn">seguid.asserts</span> <span class="kn">import</span> <span class="n">assert_in_alphabet</span>
-<span class="kn">from</span> <span class="nn">seguid.asserts</span> <span class="kn">import</span> <span class="n">assert_complementary</span>
+<span class="kn">from</span> <span class="nn">seguid._tables</span> <span class="kn">import</span> <span class="n">tablefactory</span>
+<span class="kn">from</span> <span class="nn">seguid._asserts</span> <span class="kn">import</span> <span class="n">assert_in_alphabet</span>
+<span class="kn">from</span> <span class="nn">seguid._asserts</span> <span class="kn">import</span> <span class="n">assert_complementary</span>
 
 <span class="n">seguid_prefix</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;seguid=&quot;</span>
 <span class="n">lsseguid_prefix</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;lsseguid=&quot;</span>
@@ -183,9 +183,6 @@ <h1>Source code for seguid.chksum</h1><div class="highlight"><pre>
 
 <span class="sd">    Only defined for circular sequences.</span>
 
-<span class="sd">    The srfun argument has to take a string as an argument and</span>
-<span class="sd">    return another string.</span>
-
 <span class="sd">    The checksum is prefixed with &quot;csseguid=&quot;</span>
 
 <span class="sd">    Examples</span>
@@ -217,35 +214,35 @@ <h1>Source code for seguid.chksum</h1><div class="highlight"><pre>
 <span class="w">    </span><span class="sa">r</span><span class="sd">&quot;&quot;&quot;SEGUID checksum for double stranded linear DNA (ldSEGUID).</span>
 
 <span class="sd">    Calculates the ldSEGUID checksum for a dsDNA sequence defined by two</span>
-<span class="sd">    strings representing the upper (Watson) and lower (Crick) strand</span>
-<span class="sd">    complementary DNA strands and an integer value describing the stagger</span>
-<span class="sd">    between the two strands in the 5&#39; (left) end of the molecule.</span>
+<span class="sd">    strings representing the upper (Watson) and the complementary (Crick) DNA strands.</span>
+<span class="sd">    Optional ssDNA regions in the ends are indicated by a dash &quot;-&quot; in eather strand.</span>
+<span class="sd">    Watson and Crick strands are always equal in length.</span>
 
-<span class="sd">    The algorithm first selects the lexicographically smallest</span>
-<span class="sd">    of the top or bottom strands.</span>
+<span class="sd">    The algorithm first selects the lexicographically smallest of the Watson and Crick strands.</span>
 
-<span class="sd">    The two string are joined, separated by a line break (ASCII 10) and the</span>
-<span class="sd">    lsSEGUID function is used on the resulting string.</span>
+<span class="sd">    The two string are joined 5&#39;-3&#39;, separated by a semicolon &quot;;&quot; and the lsSEGUID function</span>
+<span class="sd">    is used on the resulting string.</span>
 
 <span class="sd">    ::</span>
+
 <span class="sd">        dsDNA    ldSEGUID</span>
 
-<span class="sd">        -TATGCC  Jv9Z9JJ0IYnG-dTPBGwhDyAqnmU</span>
+<span class="sd">        -TATGCC  ldseguid=rr65d6AYuP-CdMaVmdw3L9FPt6I</span>
 <span class="sd">         |||||</span>
 <span class="sd">        CATACG-</span>
 
-<span class="sd">        -GCATAC  Jv9Z9JJ0IYnG-dTPBGwhDyAqnmU</span>
+<span class="sd">        -GCATAC  ldseguid=rr65d6AYuP-CdMaVmdw3L9FPt6I</span>
 <span class="sd">         |||||</span>
 <span class="sd">        CCGTAT-</span>
 
-<span class="sd">    For the linear dsDNA sequence defined by watson = &quot;-TATGCC&quot;, crick =&quot;-gcatac&quot;</span>
-<span class="sd">    (see figures above), The &quot;-gcatac&quot; strand is selected as</span>
-<span class="sd">    &quot;-gcatac&quot; &lt; &quot;-TATGCC&quot;.</span>
+<span class="sd">    For the linear dsDNA sequence defined by watson = &quot;-TATGCC&quot;, crick =&quot;-GCATAC&quot;</span>
+<span class="sd">    (see figures above), The &quot;-GCATAC&quot; strand is selected since lexicographically,</span>
+<span class="sd">    &quot;-GCATAC&quot; &lt; &quot;-TATGCC&quot;.</span>
 
 <span class="sd">    A string is constructed like so:</span>
 <span class="sd">    ::</span>
 
-<span class="sd">        &quot;-gcatac&quot; + chr(10) + &quot;CCGTAT-&quot;</span>
+<span class="sd">        &quot;-GCATAC&quot; + &quot;;&quot; + &quot;-TATGCC&quot;</span>
 
 <span class="sd">    The checksum is prefixed with &quot;ldseguid=&quot;</span>
 

_modules/seguid/config.html

@@ -34,7 +34,7 @@ <h1>Source code for seguid.config</h1><div class="highlight"><pre>
 <span class="c1"># -*- coding: utf-8 -*-</span>
 
 <span class="kn">import</span> <span class="nn">warnings</span>
-<span class="kn">from</span> <span class="nn">seguid.manip</span> <span class="kn">import</span> <span class="n">min_rotation_py</span>
+<span class="kn">from</span> <span class="nn">seguid._manip</span> <span class="kn">import</span> <span class="n">min_rotation_py</span>
 
 <span class="c1">## The min_rotation() function</span>
 <span class="n">_min_rotation</span> <span class="o">=</span> <span class="n">min_rotation_py</span>

_modules/seguid/reprutils.html

@@ -30,7 +30,7 @@
           <div class="body" role="main">
 
   <h1>Source code for seguid.reprutils</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">seguid.manip</span> <span class="kn">import</span> <span class="n">reverse</span>
+<span></span><span class="kn">from</span> <span class="nn">seguid._manip</span> <span class="kn">import</span> <span class="n">reverse</span>
 <span class="kn">import</span> <span class="nn">re</span>
 
 

genindex.html

@@ -33,41 +33,32 @@
 <h1 id="index">Index</h1>
 
 <div class="genindex-jumpbox">
- <a href="#A"><strong>A</strong></a>
- | <a href="#C"><strong>C</strong></a>
+ <a href="#C"><strong>C</strong></a>
  | <a href="#E"><strong>E</strong></a>
  | <a href="#I"><strong>I</strong></a>
  | <a href="#L"><strong>L</strong></a>
  | <a href="#M"><strong>M</strong></a>
  | <a href="#P"><strong>P</strong></a>
- | <a href="#R"><strong>R</strong></a>
  | <a href="#S"><strong>S</strong></a>
- | <a href="#T"><strong>T</strong></a>
 
 </div>
-<h2 id="A">A</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="index.html#seguid.asserts.assert_alphabet">assert_alphabet() (in module seguid.asserts)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="index.html#seguid.asserts.assert_complementary">assert_complementary() (in module seguid.asserts)</a>
-</li>
-      <li><a href="index.html#seguid.asserts.assert_in_alphabet">assert_in_alphabet() (in module seguid.asserts)</a>
-</li>
-  </ul></td>
-</tr></table>
-
 <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="index.html#seguid.chksum.cdseguid">cdseguid() (in module seguid.chksum)</a>
+      <li><a href="index.html#seguid.cdseguid">cdseguid() (in module seguid)</a>
+
+      <ul>
+        <li><a href="index.html#seguid.chksum.cdseguid">(in module seguid.chksum)</a>
 </li>
+      </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="index.html#seguid.chksum.csseguid">csseguid() (in module seguid.chksum)</a>
+      <li><a href="index.html#seguid.csseguid">csseguid() (in module seguid)</a>
+
+      <ul>
+        <li><a href="index.html#seguid.chksum.csseguid">(in module seguid.chksum)</a>
 </li>
+      </ul></li>
   </ul></td>
 </tr></table>
 
@@ -90,37 +81,37 @@ <h2 id="I">I</h2>
 <h2 id="L">L</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="index.html#seguid.chksum.ldseguid">ldseguid() (in module seguid.chksum)</a>
+      <li><a href="index.html#seguid.ldseguid">ldseguid() (in module seguid)</a>
+
+      <ul>
+        <li><a href="index.html#seguid.chksum.ldseguid">(in module seguid.chksum)</a>
 </li>
+      </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="index.html#seguid.chksum.lsseguid">lsseguid() (in module seguid.chksum)</a>
+      <li><a href="index.html#seguid.lsseguid">lsseguid() (in module seguid)</a>
+
+      <ul>
+        <li><a href="index.html#seguid.chksum.lsseguid">(in module seguid.chksum)</a>
 </li>
+      </ul></li>
   </ul></td>
 </tr></table>
 
 <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="index.html#seguid.manip.min_rotation_py">min_rotation_py() (in module seguid.manip)</a>
-</li>
       <li>
     module
 
       <ul>
         <li><a href="index.html#module-seguid">seguid</a>
-</li>
-        <li><a href="index.html#module-seguid.asserts">seguid.asserts</a>
 </li>
         <li><a href="index.html#module-seguid.chksum">seguid.chksum</a>
 </li>
         <li><a href="index.html#module-seguid.config">seguid.config</a>
-</li>
-        <li><a href="index.html#module-seguid.manip">seguid.manip</a>
 </li>
         <li><a href="index.html#module-seguid.reprutils">seguid.reprutils</a>
-</li>
-        <li><a href="index.html#module-seguid.tables">seguid.tables</a>
 </li>
       </ul></li>
   </ul></td>
@@ -134,24 +125,6 @@ <h2 id="P">P</h2>
   </ul></td>
 </tr></table>
 
-<h2 id="R">R</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="index.html#seguid.asserts.reverse">reverse() (in module seguid.asserts)</a>
-
-      <ul>
-        <li><a href="index.html#seguid.manip.reverse">(in module seguid.manip)</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="index.html#seguid.manip.rotate">rotate() (in module seguid.manip)</a>
-</li>
-      <li><a href="index.html#seguid.manip.rotate_to_min">rotate_to_min() (in module seguid.manip)</a>
-</li>
-  </ul></td>
-</tr></table>
-
 <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
@@ -165,62 +138,33 @@ <h2 id="S">S</h2>
       <li><a href="index.html#seguid.chksum.seguid">seguid() (in module seguid.chksum)</a>
 </li>
       <li>
-    seguid.asserts
-
-      <ul>
-        <li><a href="index.html#module-seguid.asserts">module</a>
-</li>
-      </ul></li>
-      <li>
     seguid.chksum
 
       <ul>
         <li><a href="index.html#module-seguid.chksum">module</a>
-</li>
-      </ul></li>
-      <li>
-    seguid.config
-
-      <ul>
-        <li><a href="index.html#module-seguid.config">module</a>
 </li>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>
-    seguid.manip
+    seguid.config
 
       <ul>
-        <li><a href="index.html#module-seguid.manip">module</a>
+        <li><a href="index.html#module-seguid.config">module</a>
 </li>
       </ul></li>
       <li>
     seguid.reprutils
 
       <ul>
         <li><a href="index.html#module-seguid.reprutils">module</a>
-</li>
-      </ul></li>
-      <li>
-    seguid.tables
-
-      <ul>
-        <li><a href="index.html#module-seguid.tables">module</a>
 </li>
       </ul></li>
       <li><a href="index.html#seguid.config.set_min_rotation">set_min_rotation() (in module seguid.config)</a>
 </li>
   </ul></td>
 </tr></table>
 
-<h2 id="T">T</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="index.html#seguid.tables.tablefactory">tablefactory() (in module seguid.tables)</a>
-</li>
-  </ul></td>
-</tr></table>
-
 
 
           </div>