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@julesjacobsen
julesjacobsen committed Jun 10, 2024
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288 changes: 186 additions & 102 deletions api/pheval/analyse/gene_prioritisation_analysis/index.html
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112 changes: 56 additions & 56 deletions api/pheval/post_processing/post_processing/index.html
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34 changes: 17 additions & 17 deletions developing_a_pheval_plugin/index.html
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Expand Up @@ -2690,19 +2690,19 @@ <h4 id="post-processing-methods">Post-processing methods</h4>
<tr>
<td><code>gene_symbol</code></td>
<td>
<code>str</code>
<code><span title="typing.Union">Union</span>[<span title="typing.List">List</span>[str], str]</code>
</td>
<td><p>The gene symbol for the result entry</p></td>
<td><p>The gene symbol(s) for the result entry</p></td>
<td>
<em>required</em>
</td>
</tr>
<tr>
<td><code>gene_identifier</code></td>
<td>
<code>str</code>
<code><span title="typing.Union">Union</span>[<span title="typing.List">List</span>[str], str]</code>
</td>
<td><p>The ENSEMBL gene identifier for the result entry</p></td>
<td><p>The ENSEMBL gene identifier(s) for the result entry</p></td>
<td>
<em>required</em>
</td>
Expand All @@ -2729,8 +2729,7 @@ <h4 id="post-processing-methods">Post-processing methods</h4>

<details class="quote">
<summary>Source code in <code>src/pheval/post_processing/post_processing.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">29</span>
<span class="normal">30</span>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">30</span>
<span class="normal">31</span>
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<span class="normal">33</span>
Expand All @@ -2744,21 +2743,22 @@ <h4 id="post-processing-methods">Post-processing methods</h4>
<span class="normal">41</span>
<span class="normal">42</span>
<span class="normal">43</span>
<span class="normal">44</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
<span class="normal">44</span>
<span class="normal">45</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
<span class="k">class</span> <span class="nc">PhEvalGeneResult</span><span class="p">(</span><span class="n">PhEvalResult</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Minimal data required from tool-specific output for gene prioritisation result</span>
<span class="sd"> Args:</span>
<span class="sd"> gene_symbol (str): The gene symbol for the result entry</span>
<span class="sd"> gene_identifier (str): The ENSEMBL gene identifier for the result entry</span>
<span class="sd"> gene_symbol (Union[List[str], str]): The gene symbol(s) for the result entry</span>
<span class="sd"> gene_identifier (Union[List[str], str]): The ENSEMBL gene identifier(s) for the result entry</span>
<span class="sd"> score (float): The score for the gene result entry</span>
<span class="sd"> Notes:</span>
<span class="sd"> While we recommend providing the gene identifier in the ENSEMBL namespace,</span>
<span class="sd"> any matching format used in Phenopacket interpretations is acceptable for result matching purposes</span>
<span class="sd"> in the analysis.</span>
<span class="sd"> &quot;&quot;&quot;</span>

<span class="n">gene_symbol</span><span class="p">:</span> <span class="nb">str</span>
<span class="n">gene_identifier</span><span class="p">:</span> <span class="nb">str</span>
<span class="n">gene_symbol</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="nb">str</span><span class="p">]</span>
<span class="n">gene_identifier</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="nb">str</span><span class="p">]</span>
<span class="n">score</span><span class="p">:</span> <span class="nb">float</span>
</code></pre></div></td></tr></table></div>
</details>
Expand Down Expand Up @@ -2878,8 +2878,7 @@ <h4 id="post-processing-methods">Post-processing methods</h4>

<details class="quote">
<summary>Source code in <code>src/pheval/post_processing/post_processing.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">74</span>
<span class="normal">75</span>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">75</span>
<span class="normal">76</span>
<span class="normal">77</span>
<span class="normal">78</span>
Expand All @@ -2901,7 +2900,8 @@ <h4 id="post-processing-methods">Post-processing methods</h4>
<span class="normal">94</span>
<span class="normal">95</span>
<span class="normal">96</span>
<span class="normal">97</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
<span class="normal">97</span>
<span class="normal">98</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
<span class="k">class</span> <span class="nc">PhEvalVariantResult</span><span class="p">(</span><span class="n">PhEvalResult</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Minimal data required from tool-specific output for variant prioritisation</span>
<span class="sd"> Args:</span>
Expand Down Expand Up @@ -3013,8 +3013,7 @@ <h4 id="post-processing-methods">Post-processing methods</h4>

<details class="quote">
<summary>Source code in <code>src/pheval/post_processing/post_processing.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">130</span>
<span class="normal">131</span>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">131</span>
<span class="normal">132</span>
<span class="normal">133</span>
<span class="normal">134</span>
Expand All @@ -3028,7 +3027,8 @@ <h4 id="post-processing-methods">Post-processing methods</h4>
<span class="normal">142</span>
<span class="normal">143</span>
<span class="normal">144</span>
<span class="normal">145</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
<span class="normal">145</span>
<span class="normal">146</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
<span class="k">class</span> <span class="nc">PhEvalDiseaseResult</span><span class="p">(</span><span class="n">PhEvalResult</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Minimal data required from tool-specific output for disease prioritisation</span>
<span class="sd"> Args:</span>
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2 changes: 1 addition & 1 deletion search/search_index.json
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86 changes: 43 additions & 43 deletions sitemap.xml
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Expand Up @@ -2,217 +2,217 @@
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