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| <h1>Source code for gnomad_qc.analyses.resources</h1><div class="highlight"><pre> | ||
| <span></span><span class="sd">"""Script containing gnomAD analysis resources."""</span> | ||
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| <span class="kn">import</span> <span class="nn">logging</span> | ||
| <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span> | ||
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| <span class="kn">from</span> <span class="nn">gnomad.resources.resource_utils</span> <span class="kn">import</span> <span class="n">TableResource</span> | ||
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| <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">"analysis_resources"</span><span class="p">)</span> | ||
| <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span> | ||
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| <span class="k">def</span> <span class="nf">_analysis_root</span><span class="p">(</span> | ||
| <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> | ||
| <span class="n">version</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> | ||
| <span class="n">test</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="p">)</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span> | ||
| <span class="w"> </span><span class="sd">"""</span> | ||
| <span class="sd"> Get root path to the analysis resources.</span> | ||
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| <span class="sd"> :param name: Name of the analysis.</span> | ||
| <span class="sd"> :param version: Version of the analysis path to return. Default is None, which</span> | ||
| <span class="sd"> returns no additional directory nesting.</span> | ||
| <span class="sd"> :param test: Whether to use a tmp path for analysis of the test dataset instead of</span> | ||
| <span class="sd"> the full dataset.</span> | ||
| <span class="sd"> :return: Root path of analysis resources.</span> | ||
| <span class="sd"> """</span> | ||
| <span class="n">version</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"/</span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">"</span> <span class="k">if</span> <span class="n">version</span> <span class="k">else</span> <span class="s2">""</span> | ||
| <span class="k">return</span> <span class="p">(</span> | ||
| <span class="sa">f</span><span class="s2">"gs://gnomad-tmp/gnomad_</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">_testing</span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">"</span> | ||
| <span class="k">if</span> <span class="n">test</span> | ||
| <span class="k">else</span> <span class="sa">f</span><span class="s2">"gs://gnomad/analyses/</span><span class="si">{</span><span class="n">name</span><span class="si">}{</span><span class="n">version</span><span class="si">}</span><span class="s2">"</span> | ||
| <span class="p">)</span> | ||
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| <div class="viewcode-block" id="get_pext"><a class="viewcode-back" href="../../../api_reference/analyses/resources.html#gnomad_qc.analyses.resources.get_pext">[docs]</a><span class="k">def</span> <span class="nf">get_pext</span><span class="p">(</span> | ||
| <span class="n">name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">"base_level"</span><span class="p">,</span> | ||
| <span class="n">gtex_version</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">"v10"</span><span class="p">,</span> | ||
| <span class="n">test</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="p">)</span> <span class="o">-></span> <span class="n">TableResource</span><span class="p">:</span> | ||
| <span class="w"> </span><span class="sd">"""</span> | ||
| <span class="sd"> Get pext annotation file.</span> | ||
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| <span class="sd"> :param name: Name of the pext annotation file. Default is "base_level".</span> | ||
| <span class="sd"> Must be one of ["annotation_level", "base_level", "exomes", "genomes",</span> | ||
| <span class="sd"> "browser"].</span> | ||
| <span class="sd"> :param gtex_version: GTEx version. Default is "v10".</span> | ||
| <span class="sd"> :param test: Whether to use a tmp path for analysis of the test dataset instead of</span> | ||
| <span class="sd"> the full dataset. Default is False.</span> | ||
| <span class="sd"> :return: Pext annotation file.</span> | ||
| <span class="sd"> """</span> | ||
| <span class="n">version</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"gtex_</span><span class="si">{</span><span class="n">gtex_version</span><span class="si">}</span><span class="s2">"</span> | ||
| <span class="k">return</span> <span class="n">TableResource</span><span class="p">(</span> | ||
| <span class="n">path</span><span class="o">=</span><span class="p">(</span> | ||
| <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">_analysis_root</span><span class="p">(</span><span class="s1">'pext'</span><span class="p">,</span><span class="w"> </span><span class="n">version</span><span class="o">=</span><span class="n">version</span><span class="p">,</span><span class="w"> </span><span class="n">test</span><span class="o">=</span><span class="n">test</span><span class="p">)</span><span class="si">}</span><span class="s2">/gnomad.pext.</span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">.</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">.ht"</span> | ||
| <span class="p">)</span> | ||
| <span class="p">)</span></div> | ||
| </pre></div> | ||
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