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latest/_modules/genophenocorr/analysis/_api.html

@@ -231,7 +231,7 @@ <h1>Source code for genophenocorr.analysis._api</h1><div class="highlight"><pre>
         <span class="c1"># Last, sort by corrected p value or just p value</span>
         <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="n">labeled_idx</span><span class="p">)</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_corrected_pvals</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_corrected_pvals</span><span class="o">.</span><span class="n">name</span><span class="p">))</span>
+            <span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_corrected_pvals</span><span class="o">.</span><span class="n">name</span><span class="p">),</span> <span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pvals</span><span class="o">.</span><span class="n">name</span><span class="p">)])</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pvals</span><span class="o">.</span><span class="n">name</span><span class="p">))</span></div>
 </div>

latest/_modules/genophenocorr/preprocessing/_vep.html

@@ -138,6 +138,26 @@ <h1>Source code for genophenocorr.preprocessing._vep</h1><div class="highlight">
 <span class="sd">        protein_annotator (ProteinMetadataService): a service for getting protein data</span>
 <span class="sd">        include_computational_txs (bool): Include computational transcripts, such as</span>
 <span class="sd">        RefSeq `XM_`.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">NONCODING_EFFECTS</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">UPSTREAM_GENE_VARIANT</span><span class="p">,</span>
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">FIVE_PRIME_UTR_VARIANT</span><span class="p">,</span>
+
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">NON_CODING_TRANSCRIPT_VARIANT</span><span class="p">,</span>
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">NON_CODING_TRANSCRIPT_EXON_VARIANT</span><span class="p">,</span>
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_ACCEPTOR_VARIANT</span><span class="p">,</span>
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_DONOR_VARIANT</span><span class="p">,</span>
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_DONOR_5TH_BASE_VARIANT</span><span class="p">,</span>
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_POLYPYRIMIDINE_TRACT_VARIANT</span><span class="p">,</span>
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">INTRON_VARIANT</span><span class="p">,</span>
+
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">THREE_PRIME_UTR_VARIANT</span><span class="p">,</span>
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">DOWNSTREAM_GENE_VARIANT</span><span class="p">,</span>
+        <span class="n">VariantEffect</span><span class="o">.</span><span class="n">INTERGENIC_VARIANT</span>
+    <span class="p">}</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Non-coding variant effects where we do not complain if the functional annotation lacks the protein effects.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_annotator</span><span class="p">:</span> <span class="n">ProteinMetadataService</span><span class="p">,</span>
@@ -149,7 +169,6 @@ <h1>Source code for genophenocorr.preprocessing._vep</h1><div class="highlight">
                     <span class="s1">&#39;&amp;mutfunc=1&amp;numbers=1&amp;protein=1&amp;refseq=1&amp;mane=1&#39;</span> \
                     <span class="s1">&#39;&amp;transcript_version=1&amp;variant_class=1&#39;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_include_computational_txs</span> <span class="o">=</span> <span class="n">include_computational_txs</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_slice_effects</span> <span class="o">=</span> <span class="p">[</span><span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_ACCEPTOR_VARIANT</span><span class="p">,</span> <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_DONOR_VARIANT</span><span class="p">,</span> <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_DONOR_5TH_BASE_VARIANT</span><span class="p">,</span> <span class="n">VariantEffect</span><span class="o">.</span><span class="n">SPLICE_POLYPYRIMIDINE_TRACT_VARIANT</span><span class="p">]</span>
 
 
 <div class="viewcode-block" id="VepFunctionalAnnotator.annotate">
@@ -219,7 +238,7 @@ <h1>Source code for genophenocorr.preprocessing._vep</h1><div class="highlight">
         <span class="n">protein_effect_start</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;protein_start&#39;</span><span class="p">)</span>
         <span class="n">protein_effect_end</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;protein_end&#39;</span><span class="p">)</span>
         <span class="k">if</span> <span class="n">protein_effect_start</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">protein_effect_end</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-            <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">(</span><span class="n">ve</span> <span class="ow">in</span> <span class="n">var_effects</span> <span class="k">for</span> <span class="n">ve</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_slice_effects</span><span class="p">):</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">(</span><span class="n">ve</span> <span class="ow">in</span> <span class="n">VepFunctionalAnnotator</span><span class="o">.</span><span class="n">NONCODING_EFFECTS</span> <span class="k">for</span> <span class="n">ve</span> <span class="ow">in</span> <span class="n">var_effects</span><span class="p">):</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">_logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s1">&#39;Missing start/end coordinate for </span><span class="si">%s</span><span class="s1"> on protein </span><span class="si">%s</span><span class="s1">. Protein effect will not be included.&#39;</span><span class="p">,</span> <span class="n">hgvsc_id</span><span class="p">,</span> <span class="n">protein_id</span><span class="p">)</span>
             <span class="n">protein_effect</span> <span class="o">=</span> <span class="kc">None</span>
         <span class="k">else</span><span class="p">:</span>

latest/apidocs/genophenocorr.preprocessing.html

@@ -478,6 +478,12 @@
 </ul>
 </dd>
 </dl>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="genophenocorr.preprocessing.VepFunctionalAnnotator.NONCODING_EFFECTS">
+<span class="sig-name descname"><span class="pre">NONCODING_EFFECTS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{VariantEffect.DOWNSTREAM_GENE_VARIANT,</span> <span class="pre">VariantEffect.FIVE_PRIME_UTR_VARIANT,</span> <span class="pre">VariantEffect.INTERGENIC_VARIANT,</span> <span class="pre">VariantEffect.INTRON_VARIANT,</span> <span class="pre">VariantEffect.NON_CODING_TRANSCRIPT_EXON_VARIANT,</span> <span class="pre">VariantEffect.NON_CODING_TRANSCRIPT_VARIANT,</span> <span class="pre">VariantEffect.SPLICE_ACCEPTOR_VARIANT,</span> <span class="pre">VariantEffect.SPLICE_DONOR_5TH_BASE_VARIANT,</span> <span class="pre">VariantEffect.SPLICE_DONOR_VARIANT,</span> <span class="pre">VariantEffect.SPLICE_POLYPYRIMIDINE_TRACT_VARIANT,</span> <span class="pre">VariantEffect.THREE_PRIME_UTR_VARIANT,</span> <span class="pre">VariantEffect.UPSTREAM_GENE_VARIANT}</span></em><a class="headerlink" href="#genophenocorr.preprocessing.VepFunctionalAnnotator.NONCODING_EFFECTS" title="Link to this definition"></a></dt>
+<dd><p>Non-coding variant effects where we do not complain if the functional annotation lacks the protein effects.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="genophenocorr.preprocessing.VepFunctionalAnnotator.annotate">
 <span class="sig-name descname"><span class="pre">annotate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variant_coordinates</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="genophenocorr.model.html#genophenocorr.model.VariantCoordinates" title="genophenocorr.model._variant.VariantCoordinates"><span class="pre">VariantCoordinates</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="genophenocorr.model.html#genophenocorr.model.TranscriptAnnotation" title="genophenocorr.model._variant.TranscriptAnnotation"><span class="pre">TranscriptAnnotation</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/genophenocorr/preprocessing/_vep.html#VepFunctionalAnnotator.annotate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#genophenocorr.preprocessing.VepFunctionalAnnotator.annotate" title="Link to this definition"></a></dt>

latest/genindex.html

@@ -685,6 +685,8 @@ <h2 id="N">N</h2>
       <li><a href="apidocs/genophenocorr.model.html#genophenocorr.model.VariantEffect.NON_CODING_TRANSCRIPT_EXON_VARIANT">NON_CODING_TRANSCRIPT_EXON_VARIANT (genophenocorr.model.VariantEffect attribute)</a>
 </li>
       <li><a href="apidocs/genophenocorr.model.html#genophenocorr.model.VariantEffect.NON_CODING_TRANSCRIPT_VARIANT">NON_CODING_TRANSCRIPT_VARIANT (genophenocorr.model.VariantEffect attribute)</a>
+</li>
+      <li><a href="apidocs/genophenocorr.preprocessing.html#genophenocorr.preprocessing.VepFunctionalAnnotator.NONCODING_EFFECTS">NONCODING_EFFECTS (genophenocorr.preprocessing.VepFunctionalAnnotator attribute)</a>
 </li>
       <li><a href="apidocs/genophenocorr.analysis.predicate.phenotype.html#genophenocorr.analysis.predicate.phenotype.PropagatingPhenotypePredicate.NOT_MEASURED">NOT_MEASURED (genophenocorr.analysis.predicate.phenotype.PropagatingPhenotypePredicate attribute)</a>
 </li>