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latest/_modules/genophenocorr/analysis/_config.html

@@ -92,6 +92,19 @@ <h1>Source code for genophenocorr.analysis._config</h1><div class="highlight"><p
 <span class="kn">from</span> <span class="nn">._commie</span> <span class="kn">import</span> <span class="n">CommunistCohortAnalysis</span>
 
 
+<span class="n">P_VAL_OPTIONS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;bonferroni&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">,</span> 
+                 <span class="s1">&#39;sidak&#39;</span><span class="p">,</span> <span class="s1">&#39;s&#39;</span><span class="p">,</span> 
+                 <span class="s1">&#39;holm-sidak&#39;</span><span class="p">,</span> <span class="s1">&#39;hs&#39;</span><span class="p">,</span> 
+                 <span class="s1">&#39;holm&#39;</span><span class="p">,</span> <span class="s1">&#39;h&#39;</span><span class="p">,</span> 
+                 <span class="s1">&#39;simes-hochberg&#39;</span><span class="p">,</span> <span class="s1">&#39;sh&#39;</span><span class="p">,</span> 
+                 <span class="s1">&#39;hommel&#39;</span><span class="p">,</span> <span class="s1">&#39;ho&#39;</span><span class="p">,</span> 
+                 <span class="s1">&#39;fdr_bh&#39;</span><span class="p">,</span> 
+                 <span class="s1">&#39;fdr_by&#39;</span><span class="p">,</span> 
+                 <span class="s1">&#39;fdr_tsbh&#39;</span><span class="p">,</span> 
+                 <span class="s1">&#39;fdr_tsbky&#39;</span><span class="p">,</span>
+                 <span class="s1">&#39;fdr_gbs&#39;</span><span class="p">,</span>
+                 <span class="kc">None</span><span class="p">]</span>
+
 <div class="viewcode-block" id="CohortAnalysisConfiguration">
 <a class="viewcode-back" href="../../../apidocs/genophenocorr.analysis.html#genophenocorr.analysis.CohortAnalysisConfiguration">[docs]</a>
 <span class="k">class</span> <span class="nc">CohortAnalysisConfiguration</span><span class="p">:</span>
@@ -192,8 +205,8 @@ <h1>Source code for genophenocorr.analysis._config</h1><div class="highlight"><p
         <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">missing_implies_excluded</span><span class="p">,</span> <span class="nb">bool</span><span class="p">):</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_missing_implies_excluded</span> <span class="o">=</span> <span class="n">missing_implies_excluded</span>
         <span class="k">else</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;Ignoring invalid `missing_implies_excluded` value </span><span class="si">%s</span><span class="s1">&#39;</span><span class="p">,</span>
-                                 <span class="n">missing_implies_excluded</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;Ignoring invalid `missing_implies_excluded` value </span><span class="si">%s</span><span class="s1">. Using </span><span class="si">%s</span><span class="s1">.&#39;</span><span class="p">,</span>
+                                 <span class="n">missing_implies_excluded</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_missing_implies_excluded</span><span class="p">)</span>
 
         <span class="k">return</span> <span class="bp">self</span></div>
 
@@ -204,8 +217,10 @@ <h1>Source code for genophenocorr.analysis._config</h1><div class="highlight"><p
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Set `pval_correction` option.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="c1"># TODO - check admissible values</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_pval_correction</span> <span class="o">=</span> <span class="n">pval_correction</span>
+        <span class="k">if</span> <span class="n">pval_correction</span> <span class="ow">in</span> <span class="n">P_VAL_OPTIONS</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_pval_correction</span> <span class="o">=</span> <span class="n">pval_correction</span>
+        <span class="k">else</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;Ignoring invalid `pval_correction` value </span><span class="si">%s</span><span class="s1">. Using </span><span class="si">%s</span><span class="s1"> correction.&#39;</span><span class="p">,</span> <span class="n">pval_correction</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pval_correction</span><span class="p">)</span>
         <span class="k">return</span> <span class="bp">self</span></div>
 
 
@@ -215,8 +230,16 @@ <h1>Source code for genophenocorr.analysis._config</h1><div class="highlight"><p
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Set `min_perc_patients_w_hpo` option.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="c1"># TODO - check float in range [0,1)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_min_perc_patients_w_hpo</span> <span class="o">=</span> <span class="n">min_perc_patients_w_hpo</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">min_perc_patients_w_hpo</span><span class="p">,</span> <span class="nb">float</span><span class="p">):</span>
+            <span class="k">try</span><span class="p">:</span>
+                <span class="n">min_perc_patients_w_hpo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">min_perc_patients_w_hpo</span><span class="p">)</span>
+            <span class="k">except</span> <span class="ne">ValueError</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="s2">&quot;min_perc_patients_w_hpo must be a number, but was </span><span class="si">%s</span><span class="s2">. Using </span><span class="si">%f</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">min_perc_patients_w_hpo</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_min_perc_patients_w_hpo</span><span class="p">)</span>
+                <span class="k">return</span> <span class="bp">self</span>
+        <span class="k">if</span> <span class="n">min_perc_patients_w_hpo</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="ow">or</span> <span class="n">min_perc_patients_w_hpo</span> <span class="o">&lt;=</span> <span class="mi">0</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="s2">&quot;min_perc_patients_w_hpo must be greater than 0 and at most 1, but was </span><span class="si">%f</span><span class="s2">. Using </span><span class="si">%f</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">min_perc_patients_w_hpo</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_min_perc_patients_w_hpo</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_min_perc_patients_w_hpo</span> <span class="o">=</span> <span class="n">min_perc_patients_w_hpo</span>
         <span class="k">return</span> <span class="bp">self</span></div>
 
 
@@ -229,7 +252,7 @@ <h1>Source code for genophenocorr.analysis._config</h1><div class="highlight"><p
         <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">include_sv</span><span class="p">,</span> <span class="nb">bool</span><span class="p">):</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_include_sv</span> <span class="o">=</span> <span class="n">include_sv</span>
         <span class="k">else</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;Ignoring invalid `include_sv` value </span><span class="si">%s</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">include_sv</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;Ignoring invalid `include_sv` value </span><span class="si">%s</span><span class="s1">. Using </span><span class="si">%s</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">include_sv</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_include_sv</span><span class="p">)</span>
         <span class="k">return</span> <span class="bp">self</span></div>
 
 

latest/_modules/genophenocorr/model/_cohort.html

@@ -197,7 +197,7 @@ <h1>Source code for genophenocorr.model._cohort</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="Cohort.from_patients">
 <a class="viewcode-back" href="../../../apidocs/genophenocorr.model.html#genophenocorr.model.Cohort.from_patients">[docs]</a>
     <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">from_patients</span><span class="p">(</span><span class="n">members</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">Patient</span><span class="p">],</span> <span class="n">include_patients_with_no_HPO</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">from_patients</span><span class="p">(</span><span class="n">members</span><span class="p">:</span> <span class="n">typing</span><span class="o">.</span><span class="n">Sequence</span><span class="p">[</span><span class="n">Patient</span><span class="p">],</span> <span class="n">include_patients_with_no_HPO</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">include_patients_with_no_variants</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Create a cohort from a sequence of patients.</span>
 
@@ -212,6 +212,9 @@ <h1>Source code for genophenocorr.model._cohort</h1><div class="highlight"><pre>
             <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">patient</span><span class="o">.</span><span class="n">phenotypes</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">include_patients_with_no_HPO</span><span class="p">:</span>
                 <span class="n">excluded_members</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
                 <span class="k">continue</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">patient</span><span class="o">.</span><span class="n">variants</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">include_patients_with_no_variants</span><span class="p">:</span>
+                <span class="n">excluded_members</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">patient</span><span class="p">)</span>
+                <span class="k">continue</span>
             <span class="n">cohort_phenotypes</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">patient</span><span class="o">.</span><span class="n">phenotypes</span><span class="p">)</span>
             <span class="n">cohort_variants</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">patient</span><span class="o">.</span><span class="n">variants</span><span class="p">)</span>
             <span class="n">var_counts</span><span class="o">.</span><span class="n">update</span><span class="p">([</span><span class="n">var</span><span class="o">.</span><span class="n">variant_coordinates</span><span class="o">.</span><span class="n">variant_key</span> <span class="k">for</span> <span class="n">var</span> <span class="ow">in</span> <span class="n">patient</span><span class="o">.</span><span class="n">variants</span><span class="p">])</span>

latest/_modules/genophenocorr/model/_protein.html

@@ -194,7 +194,13 @@ <h1>Source code for genophenocorr.model._protein</h1><div class="highlight"><pre
     <span class="nd">@property</span>
     <span class="nd">@abc</span><span class="o">.</span><span class="n">abstractmethod</span>
     <span class="k">def</span> <span class="nf">feature_type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">FeatureType</span><span class="p">:</span>
-        <span class="k">pass</span></div>
+        <span class="k">pass</span>
+
+<div class="viewcode-block" id="ProteinFeature.to_string">
+<a class="viewcode-back" href="../../../apidocs/genophenocorr.model.html#genophenocorr.model.ProteinFeature.to_string">[docs]</a>
+    <span class="k">def</span> <span class="nf">to_string</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">feature_type</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">-</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">info</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">-</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">info</span><span class="o">.</span><span class="n">region</span><span class="si">}</span><span class="s2">&quot;</span></div>
+</div>