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update docs to point to new lab website
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149 changes: 83 additions & 66 deletions _modules/alignparse/ccs.html
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78 changes: 36 additions & 42 deletions _modules/alignparse/minimap2.html
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Original file line number Diff line number Diff line change
@@ -1,26 +1,26 @@

<!DOCTYPE html>

<html>
<html lang="en" data-content_root="../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>alignparse.minimap2 &#8212; alignparse 0.4.0 documentation</title>
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<title>alignparse.minimap2 &#8212; alignparse 0.6.3 documentation</title>
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Expand Down Expand Up @@ -116,8 +116,10 @@ <h1>Source code for alignparse.minimap2</h1><div class="highlight"><pre>
<span class="sd">&quot;&quot;&quot;</span>


<div class="viewcode-block" id="Mapper"><a class="viewcode-back" href="../../alignparse.minimap2.html#alignparse.minimap2.Mapper">[docs]</a><span class="k">class</span> <span class="nc">Mapper</span><span class="p">:</span>
<span class="sa">r</span><span class="sd">&quot;&quot;&quot;Run `minimap2 &lt;https://lh3.github.io/minimap2/&gt;`_.</span>
<div class="viewcode-block" id="Mapper">
<a class="viewcode-back" href="../../alignparse.minimap2.html#alignparse.minimap2.Mapper">[docs]</a>
<span class="k">class</span> <span class="nc">Mapper</span><span class="p">:</span>
<span class="w"> </span><span class="sa">r</span><span class="sd">&quot;&quot;&quot;Run `minimap2 &lt;https://lh3.github.io/minimap2/&gt;`_.</span>

<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
Expand Down Expand Up @@ -187,7 +189,7 @@ <h1>Source code for alignparse.minimap2</h1><div class="highlight"><pre>
<span class="sd"> m54228_181120_212724/4194376/ccs 0 refseq 1 1 63M * 0 0</span>
<span class="sd"> ATGCAAAATGATGCATAGTATTAGCATAAATAGGATAGCCATAAGGTTACTGCATAAGAGTAT</span>
<span class="sd"> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
<span class="sd"> NM:i:4 ms:i:111 AS:i:111 nn:i:3 tp:A:P cm:i:7 s1:i:41 s2:i:0 de:f:0.0167</span>
<span class="sd"> NM:i:4 ms:i:111 AS:i:111 nn:i:3 tp:A:P cm:i:7 s1:i:41 s2:i:0 de:f:0.0635</span>
<span class="sd"> cs:Z::6*na*na*nt:49*ga:4 rl:i:0</span>
<span class="sd"> &gt;&gt;&gt; print(tag_names)</span>
<span class="sd"> [&#39;NM&#39;, &#39;ms&#39;, &#39;AS&#39;, &#39;nn&#39;, &#39;tp&#39;, &#39;cm&#39;, &#39;s1&#39;, &#39;s2&#39;, &#39;de&#39;, &#39;cs&#39;, &#39;rl&#39;]</span>
Expand All @@ -203,7 +205,7 @@ <h1>Source code for alignparse.minimap2</h1><div class="highlight"><pre>
<span class="sd"> m54228_181120_212724/4194376/ccs 0 refseq 1 1 63M * 0 0</span>
<span class="sd"> ATGCAAAATGATGCATAGTATTAGCATAAATAGGATAGCCATAAGGTTACTGCATAAGAGTAT</span>
<span class="sd"> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
<span class="sd"> NM:i:4 ms:i:111 AS:i:111 nn:i:3 tp:A:P cm:i:7 s1:i:41 s2:i:0 de:f:0.0167</span>
<span class="sd"> NM:i:4 ms:i:111 AS:i:111 nn:i:3 tp:A:P cm:i:7 s1:i:41 s2:i:0 de:f:0.0635</span>
<span class="sd"> cs:Z::6*na*na*nt:49*ga:4 rl:i:0 np:i:127</span>
<span class="sd"> &gt;&gt;&gt; print(tag_names) # doctest: +NORMALIZE_WHITESPACE</span>
<span class="sd"> [&#39;NM&#39;, &#39;ms&#39;, &#39;AS&#39;, &#39;nn&#39;, &#39;tp&#39;, &#39;cm&#39;, &#39;s1&#39;, &#39;s2&#39;, &#39;de&#39;, &#39;cs&#39;, &#39;rl&#39;, &#39;np&#39;]</span>
Expand All @@ -223,7 +225,7 @@ <h1>Source code for alignparse.minimap2</h1><div class="highlight"><pre>
<span class="n">check_cs</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">retain_tags</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="p">):</span>
<span class="sd">&quot;&quot;&quot;See main :class:`Mapper` doc string.&quot;&quot;&quot;</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;See main :class:`Mapper` doc string.&quot;&quot;&quot;</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">version</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">check_output</span><span class="p">([</span><span class="n">prog</span><span class="p">,</span> <span class="s2">&quot;--version&quot;</span><span class="p">])</span>
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
Expand All @@ -247,8 +249,10 @@ <h1>Source code for alignparse.minimap2</h1><div class="highlight"><pre>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">retain_tags</span> <span class="o">=</span> <span class="kc">None</span>

<div class="viewcode-block" id="Mapper.map_to_sam"><a class="viewcode-back" href="../../alignparse.minimap2.html#alignparse.minimap2.Mapper.map_to_sam">[docs]</a> <span class="k">def</span> <span class="nf">map_to_sam</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">targetfile</span><span class="p">,</span> <span class="n">queryfile</span><span class="p">,</span> <span class="n">samfile</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Map query sequences to targets and output SAM file.</span>
<div class="viewcode-block" id="Mapper.map_to_sam">
<a class="viewcode-back" href="../../alignparse.minimap2.html#alignparse.minimap2.Mapper.map_to_sam">[docs]</a>
<span class="k">def</span> <span class="nf">map_to_sam</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">targetfile</span><span class="p">,</span> <span class="n">queryfile</span><span class="p">,</span> <span class="n">samfile</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Map query sequences to targets and output SAM file.</span>

<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
Expand All @@ -262,7 +266,7 @@ <h1>Source code for alignparse.minimap2</h1><div class="highlight"><pre>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">for</span> <span class="n">fname</span><span class="p">,</span> <span class="n">f</span> <span class="ow">in</span> <span class="p">[(</span><span class="s2">&quot;target&quot;</span><span class="p">,</span> <span class="n">targetfile</span><span class="p">),</span> <span class="p">(</span><span class="s2">&quot;query&quot;</span><span class="p">,</span> <span class="n">queryfile</span><span class="p">)]:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">IOError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;cannot find `</span><span class="si">{</span><span class="n">fname</span><span class="si">}</span><span class="s2">file` </span><span class="si">{</span><span class="n">f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">raise</span> <span class="ne">OSError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;cannot find `</span><span class="si">{</span><span class="n">fname</span><span class="si">}</span><span class="s2">file` </span><span class="si">{</span><span class="n">f</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>

<span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">samfile</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">!=</span> <span class="s2">&quot;.sam&quot;</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;`samfile` lacks extension &#39;.sam&#39;: </span><span class="si">{</span><span class="n">samfile</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
Expand All @@ -283,7 +287,7 @@ <h1>Source code for alignparse.minimap2</h1><div class="highlight"><pre>
<span class="c1"># do the alignment</span>
<span class="k">with</span> <span class="n">contextlib</span><span class="o">.</span><span class="n">ExitStack</span><span class="p">()</span> <span class="k">as</span> <span class="n">stack</span><span class="p">:</span>
<span class="n">sam</span> <span class="o">=</span> <span class="n">stack</span><span class="o">.</span><span class="n">enter_context</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">untagged_samfile</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">))</span>
<span class="n">err</span> <span class="o">=</span> <span class="n">stack</span><span class="o">.</span><span class="n">enter_context</span><span class="p">(</span><span class="n">tempfile</span><span class="o">.</span><span class="n">TemporaryFile</span><span class="p">(</span><span class="n">mode</span><span class="o">=</span><span class="s2">&quot;w&quot;</span><span class="p">))</span>
<span class="n">err</span> <span class="o">=</span> <span class="n">stack</span><span class="o">.</span><span class="n">enter_context</span><span class="p">(</span><span class="n">tempfile</span><span class="o">.</span><span class="n">TemporaryFile</span><span class="p">(</span><span class="n">mode</span><span class="o">=</span><span class="s2">&quot;w+&quot;</span><span class="p">))</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">_</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">check_call</span><span class="p">(</span><span class="n">cmds</span><span class="p">,</span> <span class="n">stdout</span><span class="o">=</span><span class="n">sam</span><span class="p">,</span> <span class="n">stderr</span><span class="o">=</span><span class="n">err</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">exc</span><span class="p">:</span>
Expand Down Expand Up @@ -352,7 +356,9 @@ <h1>Source code for alignparse.minimap2</h1><div class="highlight"><pre>
<span class="p">)</span>
<span class="n">tagged_sam</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>

<span class="k">assert</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">samfile</span><span class="p">)</span></div></div>
<span class="k">assert</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">samfile</span><span class="p">)</span></div>
</div>



<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
Expand All @@ -365,11 +371,11 @@ <h1>Source code for alignparse.minimap2</h1><div class="highlight"><pre>

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Expand All @@ -392,18 +398,6 @@ <h1 class="logo logo-name">alignparse</h1>





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Expand All @@ -425,16 +419,16 @@ <h3>Related Topics</h3>
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Expand All @@ -448,17 +442,17 @@ <h3 id="searchlabel">Quick search</h3>
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