update docs

mortazavilab · Dec 4, 2023 · 3269e7f · 3269e7f
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diff --git a/docs/doctrees/api.doctree b/docs/doctrees/api.doctree
diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/html/_modules/PyWGCNA/utils.html b/docs/html/_modules/PyWGCNA/utils.html
@@ -108,6 +108,7 @@ <h1>Source code for PyWGCNA.utils</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span> <span class="nn">pickle</span>
 <span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">import</span> <span class="nn">biomart</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
 <span class="kn">import</span> <span class="nn">requests</span>
 <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 <span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
@@ -230,10 +231,11 @@ <h1>Source code for PyWGCNA.utils</h1><div class="highlight"><pre>
     <span class="c1"># Store the data in a dict</span>
     <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">data</span><span class="o">.</span><span class="n">splitlines</span><span class="p">():</span>
         <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="n">tmp</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="n">attributes</span><span class="p">)</span><span class="o">.</span><span class="n">T</span>
         <span class="nb">dict</span> <span class="o">=</span> <span class="p">{}</span>
         <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">attributes</span><span class="p">)):</span>
             <span class="nb">dict</span><span class="p">[</span><span class="n">attributes</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
-        <span class="n">geneInfo</span> <span class="o">=</span> <span class="n">geneInfo</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="n">geneInfo</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">geneInfo</span><span class="p">,</span> <span class="n">tmp</span><span class="p">],</span> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 
     <span class="n">geneInfo</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">geneInfo</span><span class="p">[</span><span class="n">attributes</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
     <span class="n">geneInfo</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">attributes</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>