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@yaseminbridges
yaseminbridges committed Jan 16, 2025
1 parent 873b603 commit 1309459
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14 changes: 11 additions & 3 deletions api/pheval/prepare/prepare_corpus/index.html
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Expand Up @@ -1541,7 +1541,11 @@ <h2 id="src.pheval.prepare.prepare_corpus.prepare_corpus" class="doc doc-heading
<span class="normal">92</span>
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<span class="normal">95</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">prepare_corpus</span><span class="p">(</span>
<span class="normal">95</span>
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<span class="normal">99</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">prepare_corpus</span><span class="p">(</span>
<span class="n">phenopacket_dir</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span>
<span class="n">variant_analysis</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span>
<span class="n">gene_analysis</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span>
Expand Down Expand Up @@ -1621,8 +1625,12 @@ <h2 id="src.pheval.prepare.prepare_corpus.prepare_corpus" class="doc doc-heading
<span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="c1"># if not updating phenopacket gene identifiers then copy phenopacket as is to output directory</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span>
<span class="n">phenopacket_path</span><span class="p">,</span> <span class="n">output_dir</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;phenopackets/</span><span class="si">{</span><span class="n">phenopacket_path</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="p">(</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span>
<span class="n">phenopacket_path</span><span class="p">,</span> <span class="n">output_dir</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;phenopackets/</span><span class="si">{</span><span class="n">phenopacket_path</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">phenopacket_path</span> <span class="o">!=</span> <span class="n">output_dir</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;phenopackets/</span><span class="si">{</span><span class="n">phenopacket_path</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">else</span> <span class="kc">None</span>
<span class="p">)</span>
</code></pre></div></td></tr></table></div>
</details>
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2 changes: 1 addition & 1 deletion search/search_index.json
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88 changes: 44 additions & 44 deletions sitemap.xml
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Expand Up @@ -2,178 +2,178 @@
<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
<url>
<loc>https://monarch-initiative.github.io/pheval/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/CODE_OF_CONDUCT/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/about/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/contact/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/contributing/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/developing_a_pheval_plugin/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/executing_a_benchmark/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/exomiser_pipeline/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/pipeline/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/plugins/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/roadmap/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/styleguide/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/cli/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/config_parser/</loc>
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<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/run_metadata/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/analysis/</loc>
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<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/assess_prioritisation_base/</loc>
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<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/benchmark_db_manager/</loc>
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<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/benchmark_generator/</loc>
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<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/benchmarking_data/</loc>
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<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/disease_prioritisation_analysis/</loc>
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<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/gene_prioritisation_analysis/</loc>
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<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/generate_plots/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/generate_summary_outputs/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/parse_benchmark_summary/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/parse_corpus/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/prioritisation_result_types/</loc>
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<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/rank_stats/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/run_data_parser/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/analyse/variant_prioritisation_analysis/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/infra/exomiserdb/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/post_processing/post_processing/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/prepare/create_noisy_phenopackets/</loc>
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<lastmod>2025-01-16</lastmod>
</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/prepare/create_spiked_vcf/</loc>
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<lastmod>2025-01-16</lastmod>
</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/prepare/custom_exceptions/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/prepare/prepare_corpus/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/prepare/update_phenopacket/</loc>
<lastmod>2025-01-07</lastmod>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/runners/runner/</loc>
<lastmod>2025-01-07</lastmod>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/utils/exomiser/</loc>
<lastmod>2025-01-07</lastmod>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/utils/file_utils/</loc>
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<lastmod>2025-01-16</lastmod>
</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/utils/phenopacket_utils/</loc>
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<lastmod>2025-01-16</lastmod>
</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/utils/semsim_utils/</loc>
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</url>
<url>
<loc>https://monarch-initiative.github.io/pheval/api/pheval/utils/utils/</loc>
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</url>
</urlset>
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