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latest/_modules/gpsea/view/_protein_visualizable.html

@@ -119,6 +119,8 @@ <h1>Source code for gpsea.view._protein_visualizable</h1><div class="highlight">
         <span class="n">variant_regions_on_protein</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">List</span><span class="p">[</span><span class="n">Region</span><span class="p">]</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_variant_effect</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
         <span class="k">for</span> <span class="n">tx_ann</span> <span class="ow">in</span> <span class="n">transcript_annotations</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">tx_ann</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">continue</span>
             <span class="n">variant_effects</span> <span class="o">=</span> <span class="n">tx_ann</span><span class="o">.</span><span class="n">variant_effects</span>
             <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">variant_effects</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
                 <span class="k">continue</span>
@@ -162,24 +164,19 @@ <h1>Source code for gpsea.view._protein_visualizable</h1><div class="highlight">
     <span class="k">def</span><span class="w"> </span><span class="nf">_get_tx_anns</span><span class="p">(</span>
         <span class="n">variants</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Iterable</span><span class="p">[</span><span class="n">Variant</span><span class="p">],</span>
         <span class="n">protein_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">TranscriptAnnotation</span><span class="p">]:</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">typing</span><span class="o">.</span><span class="n">Optional</span><span class="p">[</span><span class="n">TranscriptAnnotation</span><span class="p">]]:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        By default, the API returns transcript annotations for many transcripts.</span>
 <span class="sd">        We would like to store the annotations only for our protein of interest (protein_id)</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">tx_anns</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">variants</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">variants</span><span class="p">:</span>
             <span class="n">tx_ann</span> <span class="o">=</span> <span class="kc">None</span>
             <span class="k">for</span> <span class="n">ann</span> <span class="ow">in</span> <span class="n">v</span><span class="o">.</span><span class="n">tx_annotations</span><span class="p">:</span>
                 <span class="k">if</span> <span class="n">ann</span><span class="o">.</span><span class="n">protein_id</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">ann</span><span class="o">.</span><span class="n">protein_id</span> <span class="o">==</span> <span class="n">protein_id</span><span class="p">:</span>
                     <span class="n">tx_ann</span> <span class="o">=</span> <span class="n">ann</span>
                     <span class="k">break</span>
-            <span class="k">if</span> <span class="n">tx_ann</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                    <span class="sa">f</span><span class="s2">&quot;The transcript annotation for </span><span class="si">{</span><span class="n">protein_id</span><span class="si">}</span><span class="s2"> was not found!&quot;</span>
-                <span class="p">)</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="n">tx_anns</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tx_ann</span><span class="p">)</span>
+            <span class="n">tx_anns</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tx_ann</span><span class="p">)</span>
 
         <span class="k">return</span> <span class="n">tx_anns</span>
 

latest/_modules/gpsea/view/_viewers.html

@@ -620,12 +620,10 @@ <h1>Source code for gpsea.view._viewers</h1><div class="highlight"><pre>
     <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">protein_metadata</span><span class="p">:</span> <span class="n">ProteinMetadata</span><span class="p">,</span>
-        <span class="n">tx_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
     <span class="p">):</span>
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_cohort_template</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_environment</span><span class="o">.</span><span class="n">get_template</span><span class="p">(</span><span class="s2">&quot;protein.html&quot;</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_protein_meta</span> <span class="o">=</span> <span class="n">protein_metadata</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_tx_id</span> <span class="o">=</span> <span class="n">tx_id</span>
 
 <div class="viewcode-block" id="ProteinVariantViewer.process">
 <a class="viewcode-back" href="../../../apidocs/gpsea.view.html#gpsea.view.ProteinVariantViewer.process">[docs]</a>
@@ -662,7 +660,7 @@ <h1>Source code for gpsea.view._viewers</h1><div class="highlight"><pre>
         <span class="c1"># not over *unique* `VariantInfo`s</span>
         <span class="k">for</span> <span class="n">var</span> <span class="ow">in</span> <span class="n">cohort</span><span class="o">.</span><span class="n">all_variants</span><span class="p">():</span>
             <span class="n">target_annot</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span>
-                <span class="p">(</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">var</span><span class="o">.</span><span class="n">tx_annotations</span> <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">transcript_id</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">_tx_id</span><span class="p">),</span> <span class="kc">None</span>
+                <span class="p">(</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">var</span><span class="o">.</span><span class="n">tx_annotations</span> <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">protein_id</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">_protein_meta</span><span class="o">.</span><span class="n">protein_id</span><span class="p">),</span> <span class="kc">None</span>
             <span class="p">)</span>
             <span class="k">if</span> <span class="n">target_annot</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
                 <span class="c1"># structural variants do not have a transcript id, and we skip them</span>

latest/_sources/user-guide/exploratory.rst.txt

@@ -148,7 +148,7 @@ This code will produce the following table on the basis of a cohort of individua
 with variants in the *TBX5* gene:
 
 >>> from gpsea.view import ProteinVariantViewer
->>> cpd_viewer = ProteinVariantViewer(tx_id=tx_id, protein_metadata=protein_meta)
+>>> cpd_viewer = ProteinVariantViewer(protein_metadata=protein_meta)
 >>> report = cpd_viewer.process(cohort)
 >>> report  # doctest: +SKIP
 

latest/apidocs/gpsea.view.html

@@ -371,7 +371,7 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="gpsea.view.ProteinVariantViewer">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.view.</span></span><span class="sig-name descname"><span class="pre">ProteinVariantViewer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_metadata</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.model.html#gpsea.model.ProteinMetadata" title="gpsea.model._protein.ProteinMetadata"><span class="pre">ProteinMetadata</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">tx_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/view/_viewers.html#ProteinVariantViewer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.view.ProteinVariantViewer" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gpsea.view.</span></span><span class="sig-name descname"><span class="pre">ProteinVariantViewer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_metadata</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="gpsea.model.html#gpsea.model.ProteinMetadata" title="gpsea.model._protein.ProteinMetadata"><span class="pre">ProteinMetadata</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/view/_viewers.html#ProteinVariantViewer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.view.ProteinVariantViewer" title="Link to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="#gpsea.view.BaseViewer" title="gpsea.view._base.BaseViewer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseViewer</span></code></a></p>
 <p>Class to create a pretty HTML table to display the protein information in the Jupyter notebook.</p>
 <dl class="py method">

latest/user-guide/exploratory.html

@@ -660,7 +660,7 @@ <h3>Distribution of variants across protein domains<a class="headerlink" href="#
 <p>This code will produce the following table on the basis of a cohort of individuals
 with variants in the <em>TBX5</em> gene:</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">gpsea.view</span><span class="w"> </span><span class="kn">import</span> <span class="n">ProteinVariantViewer</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">cpd_viewer</span> <span class="o">=</span> <span class="n">ProteinVariantViewer</span><span class="p">(</span><span class="n">tx_id</span><span class="o">=</span><span class="n">tx_id</span><span class="p">,</span> <span class="n">protein_metadata</span><span class="o">=</span><span class="n">protein_meta</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">cpd_viewer</span> <span class="o">=</span> <span class="n">ProteinVariantViewer</span><span class="p">(</span><span class="n">protein_metadata</span><span class="o">=</span><span class="n">protein_meta</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">report</span> <span class="o">=</span> <span class="n">cpd_viewer</span><span class="o">.</span><span class="n">process</span><span class="p">(</span><span class="n">cohort</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">report</span>  
 </pre></div>