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@@ -1,21 +1,23 @@
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+  <title>gffutils.biopython_integration &mdash; gffutils 0.13 documentation</title>
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@@ -33,7 +35,7 @@
             gffutils
           </a>
               <div class="version">
-                0.12
+                0.13
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@@ -87,7 +89,6 @@ <h1>Source code for gffutils.biopython_integration</h1><div class="highlight"><p
 <span class="sd">Module for integration with BioPython, specifically SeqRecords and SeqFeature</span>
 <span class="sd">objects.</span>
 <span class="sd">&quot;&quot;&quot;</span>
-<span class="kn">import</span> <span class="nn">six</span>
 
 <span class="k">try</span><span class="p">:</span>
     <span class="kn">from</span> <span class="nn">Bio.SeqFeature</span> <span class="kn">import</span> <span class="n">SeqFeature</span><span class="p">,</span> <span class="n">FeatureLocation</span>
@@ -100,12 +101,15 @@ <h1>Source code for gffutils.biopython_integration</h1><div class="highlight"><p
 <span class="n">_biopython_strand</span> <span class="o">=</span> <span class="p">{</span>
     <span class="s2">&quot;+&quot;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
     <span class="s2">&quot;-&quot;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
-    <span class="s2">&quot;.&quot;</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+    <span class="s2">&quot;.&quot;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="s2">&quot;?&quot;</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
 <span class="p">}</span>
 <span class="n">_feature_strand</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">v</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">_biopython_strand</span><span class="o">.</span><span class="n">items</span><span class="p">())</span>
 
 
-<div class="viewcode-block" id="to_seqfeature"><a class="viewcode-back" href="../../autodocs/gffutils.biopython_integration.to_seqfeature.html#gffutils.biopython_integration.to_seqfeature">[docs]</a><span class="k">def</span> <span class="nf">to_seqfeature</span><span class="p">(</span><span class="n">feature</span><span class="p">):</span>
+<div class="viewcode-block" id="to_seqfeature">
+<a class="viewcode-back" href="../../autodocs/gffutils.biopython_integration.to_seqfeature.html#gffutils.biopython_integration.to_seqfeature">[docs]</a>
+<span class="k">def</span> <span class="nf">to_seqfeature</span><span class="p">(</span><span class="n">feature</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Converts a gffutils.Feature object to a Bio.SeqFeature object.</span>
 
@@ -118,7 +122,7 @@ <h1>Source code for gffutils.biopython_integration</h1><div class="highlight"><p
 <span class="sd">        If string, assume it is a GFF or GTF-format line; otherwise just use</span>
 <span class="sd">        the provided feature directly.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">feature</span><span class="p">,</span> <span class="n">six</span><span class="o">.</span><span class="n">string_types</span><span class="p">):</span>
+    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">feature</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
         <span class="n">feature</span> <span class="o">=</span> <span class="n">feature_from_line</span><span class="p">(</span><span class="n">feature</span><span class="p">)</span>
 
     <span class="n">qualifiers</span> <span class="o">=</span> <span class="p">{</span>
@@ -131,15 +135,19 @@ <h1>Source code for gffutils.biopython_integration</h1><div class="highlight"><p
     <span class="k">return</span> <span class="n">SeqFeature</span><span class="p">(</span>
         <span class="c1"># Convert from GFF 1-based to standard Python 0-based indexing used by</span>
         <span class="c1"># BioPython</span>
-        <span class="n">FeatureLocation</span><span class="p">(</span><span class="n">feature</span><span class="o">.</span><span class="n">start</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="n">feature</span><span class="o">.</span><span class="n">stop</span><span class="p">),</span>
+        <span class="n">FeatureLocation</span><span class="p">(</span>
+            <span class="n">feature</span><span class="o">.</span><span class="n">start</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="n">feature</span><span class="o">.</span><span class="n">stop</span><span class="p">,</span> <span class="n">strand</span><span class="o">=</span><span class="n">_biopython_strand</span><span class="p">[</span><span class="n">feature</span><span class="o">.</span><span class="n">strand</span><span class="p">]</span>
+        <span class="p">),</span>
         <span class="nb">id</span><span class="o">=</span><span class="n">feature</span><span class="o">.</span><span class="n">id</span><span class="p">,</span>
         <span class="nb">type</span><span class="o">=</span><span class="n">feature</span><span class="o">.</span><span class="n">featuretype</span><span class="p">,</span>
-        <span class="n">strand</span><span class="o">=</span><span class="n">_biopython_strand</span><span class="p">[</span><span class="n">feature</span><span class="o">.</span><span class="n">strand</span><span class="p">],</span>
         <span class="n">qualifiers</span><span class="o">=</span><span class="n">qualifiers</span><span class="p">,</span>
     <span class="p">)</span></div>
 
 
-<div class="viewcode-block" id="from_seqfeature"><a class="viewcode-back" href="../../autodocs/gffutils.biopython_integration.from_seqfeature.html#gffutils.biopython_integration.from_seqfeature">[docs]</a><span class="k">def</span> <span class="nf">from_seqfeature</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+<div class="viewcode-block" id="from_seqfeature">
+<a class="viewcode-back" href="../../autodocs/gffutils.biopython_integration.from_seqfeature.html#gffutils.biopython_integration.from_seqfeature">[docs]</a>
+<span class="k">def</span> <span class="nf">from_seqfeature</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Converts a Bio.SeqFeature object to a gffutils.Feature object.</span>
 
@@ -151,12 +159,12 @@ <h1>Source code for gffutils.biopython_integration</h1><div class="highlight"><p
     <span class="n">score</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">qualifiers</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;score&quot;</span><span class="p">,</span> <span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
     <span class="n">seqid</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">qualifiers</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;seqid&quot;</span><span class="p">,</span> <span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
     <span class="n">frame</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">qualifiers</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;frame&quot;</span><span class="p">,</span> <span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
-    <span class="n">strand</span> <span class="o">=</span> <span class="n">_feature_strand</span><span class="p">[</span><span class="n">s</span><span class="o">.</span><span class="n">strand</span><span class="p">]</span>
+    <span class="n">strand</span> <span class="o">=</span> <span class="n">_feature_strand</span><span class="p">[</span><span class="n">s</span><span class="o">.</span><span class="n">location</span><span class="o">.</span><span class="n">strand</span><span class="p">]</span>
 
     <span class="c1"># BioPython parses 1-based GenBank positions into 0-based for use within</span>
     <span class="c1"># Python.  We need to convert back to 1-based GFF format here.</span>
-    <span class="n">start</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">location</span><span class="o">.</span><span class="n">start</span><span class="o">.</span><span class="n">position</span> <span class="o">+</span> <span class="mi">1</span>
-    <span class="n">stop</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">location</span><span class="o">.</span><span class="n">end</span><span class="o">.</span><span class="n">position</span>
+    <span class="n">start</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">location</span><span class="o">.</span><span class="n">start</span> <span class="o">+</span> <span class="mi">1</span>
+    <span class="n">stop</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">location</span><span class="o">.</span><span class="n">end</span>
     <span class="n">featuretype</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">type</span>
     <span class="nb">id</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">id</span>
     <span class="n">attributes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">qualifiers</span><span class="p">)</span>
@@ -177,6 +185,7 @@ <h1>Source code for gffutils.biopython_integration</h1><div class="highlight"><p
         <span class="nb">id</span><span class="o">=</span><span class="nb">id</span><span class="p">,</span>
         <span class="o">**</span><span class="n">kwargs</span>
     <span class="p">)</span></div>
+
 </pre></div>
 
            </div>