---

title: Runner module

keywords: fastai
sidebar: home_sidebar

summary: "The format functions"
description: "The format functions"
nb_path: "nbs/04_Runner.ipynb"
---
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<h4 id="format" class="doc_header"><code>format</code><a href="__main__.py#L18" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>format</code>(<strong><code>tpeds</code></strong>, <strong><code>tfam</code></strong>, <strong><code>prev</code></strong>=<em><code>None</code></em>, <strong><code>wild_pen</code></strong>=<em><code>None</code></em>, <strong><code>muta_pen</code></strong>=<em><code>None</code></em>, <strong><code>out_format</code></strong>=<em><code>'MERLIN'</code></em>, <strong><code>inherit_mode</code></strong>=<em><code>None</code></em>, <strong><code>theta_max</code></strong>=<em><code>None</code></em>, <strong><code>theta_inc</code></strong>=<em><code>None</code></em>)</p>
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<h4 id="format_plink" class="doc_header"><code>format_plink</code><a href="__main__.py#L33" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>format_plink</code>(<strong><code>tped</code></strong>, <strong><code>tfam</code></strong>)</p>
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<h4 id="format_mega2" class="doc_header"><code>format_mega2</code><a href="__main__.py#L50" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>format_mega2</code>(<strong><code>tped</code></strong>, <strong><code>tfam</code></strong>)</p>
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<h4 id="format_merlin" class="doc_header"><code>format_merlin</code><a href="__main__.py#L89" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>format_merlin</code>(<strong><code>tped</code></strong>, <strong><code>tfam</code></strong>)</p>
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<h4 id="format_linkage" class="doc_header"><code>format_linkage</code><a href="__main__.py#L133" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>format_linkage</code>(<strong><code>tped</code></strong>, <strong><code>tfam</code></strong>, <strong><code>prev</code></strong>, <strong><code>wild_pen</code></strong>, <strong><code>muta_pen</code></strong>, <strong><code>inherit_mode</code></strong>, <strong><code>theta_max</code></strong>, <strong><code>theta_inc</code></strong>)</p>
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<h4 id="parse_tfam" class="doc_header"><code>parse_tfam</code><a href="__main__.py#L210" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>parse_tfam</code>(<strong><code>fh</code></strong>)</p>
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<h2 id="Pedigree" class="doc_header"><code>class</code> <code>Pedigree</code><a href="" class="source_link" style="float:right">[source]</a></h2><blockquote><p><code>Pedigree</code>()</p>
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<h4 id="run_linkage" class="doc_header"><code>run_linkage</code><a href="__main__.py#L270" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>run_linkage</code>(<strong><code>blueprint</code></strong>, <strong><code>theta_inc</code></strong>, <strong><code>theta_max</code></strong>, <strong><code>to_plot</code></strong>=<em><code>True</code></em>)</p>
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<h4 id="linkage_worker" class="doc_header"><code>linkage_worker</code><a href="__main__.py#L279" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>linkage_worker</code>(<strong><code>blueprint</code></strong>, <strong><code>workdir</code></strong>, <strong><code>theta_inc</code></strong>, <strong><code>theta_max</code></strong>, <strong><code>errfile</code></strong>, <strong><code>to_plot</code></strong>=<em><code>True</code></em>)</p>
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<h4 id="hinton" class="doc_header"><code>hinton</code><a href="__main__.py#L400" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>hinton</code>(<strong><code>filename</code></strong>, <strong><code>max_weight</code></strong>=<em><code>None</code></em>, <strong><code>ax</code></strong>=<em><code>None</code></em>)</p>
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<h4 id="heatmap" class="doc_header"><code>heatmap</code><a href="__main__.py#L423" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>heatmap</code>(<strong><code>file</code></strong>, <strong><code>theta_inc</code></strong>, <strong><code>theta_max</code></strong>)</p>
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<h4 id="hlod_fun" class="doc_header"><code>hlod_fun</code><a href="__main__.py#L449" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>hlod_fun</code>(<strong><code>Li</code></strong>, <strong><code>sign</code></strong>=<em><code>1</code></em>)</p>
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<h4 id="html" class="doc_header"><code>html</code><a href="__main__.py#L454" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>html</code>(<strong><code>theta_inc</code></strong>, <strong><code>theta_max</code></strong>, <strong><code>limit</code></strong>)</p>
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<h4 id="html_img" class="doc_header"><code>html_img</code><a href="__main__.py#L532" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>html_img</code>(<strong><code>ltype</code></strong>)</p>
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<h4 id="html_table" class="doc_header"><code>html_table</code><a href="__main__.py#L538" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>html_table</code>(<strong><code>type</code></strong>, <strong><code>theta_inc</code></strong>, <strong><code>theta_max</code></strong>, <strong><code>limit</code></strong>)</p>
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