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Author: Camille Scott <[email protected]>

    A bunch of fixes brought in from 1.0 branch, update to reqs, version bump
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camillescott committed Nov 23, 2016
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48 changes: 25 additions & 23 deletions doc/_build/html/_modules/dammit/blast.html
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Expand Up @@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />

<title>dammit.blast &mdash; dammit 0.3 documentation</title>
<title>dammit.blast &#8212; dammit 0.3.1 documentation</title>

<link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
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Expand All @@ -15,7 +15,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../',
VERSION: '0.3',
VERSION: '0.3.1',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
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<h1>Source code for dammit.blast</h1><div class="highlight"><pre>
<span class="c">#!/usr/bin/env python</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
<span></span><span class="ch">#!/usr/bin/env python</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">csv</span>
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="kn">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>


<div class="viewcode-block" id="fix_coords_single"><a class="viewcode-back" href="../../dammit.html#dammit.blast.fix_coords_single">[docs]</a><span class="k">def</span> <span class="nf">fix_coords_single</span><span class="p">(</span><span class="n">sstart</span><span class="p">,</span> <span class="n">send</span><span class="p">,</span> <span class="n">qstart</span><span class="p">,</span> <span class="n">qend</span><span class="p">):</span>
Expand All @@ -60,7 +65,7 @@ <h1>Source code for dammit.blast</h1><div class="highlight"><pre>
<span class="sd"> ndarray: Numpy array with values [sstart, send, qstart, qend, sstrand, qstrand],</span>
<span class="sd"> where sstrand and qstrand are the subject and query strands as a 1 or -1.</span>
<span class="sd"> &#39;&#39;&#39;</span>
<span class="n">res</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">(</span><span class="mi">6</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">long</span><span class="p">)</span>
<span class="n">res</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">(</span><span class="mi">6</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">long</span><span class="p">)</span>

<span class="k">if</span> <span class="n">sstart</span> <span class="o">&lt;</span> <span class="n">send</span><span class="p">:</span>
<span class="n">res</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">sstart</span> <span class="o">-</span> <span class="mi">1</span>
Expand Down Expand Up @@ -96,20 +101,20 @@ <h1>Source code for dammit.blast</h1><div class="highlight"><pre>
<span class="sd"> &#39;&#39;&#39;</span>
<span class="n">n</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">sstart</span><span class="p">)</span>
<span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">res</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">((</span><span class="n">n</span><span class="p">,</span><span class="mi">6</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">long</span><span class="p">)</span>
<span class="n">res</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">((</span><span class="n">n</span><span class="p">,</span><span class="mi">6</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="n">long</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n</span><span class="p">):</span>
<span class="n">res</span><span class="p">[</span><span class="n">i</span><span class="p">,:]</span> <span class="o">=</span> <span class="n">fix_coords_single</span><span class="p">(</span><span class="n">sstart</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">send</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">qstart</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">qend</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
<span class="k">return</span> <span class="n">res</span></div>


<div class="viewcode-block" id="remap_blast_coords_df"><a class="viewcode-back" href="../../dammit.html#dammit.blast.remap_blast_coords_df">[docs]</a><span class="k">def</span> <span class="nf">remap_blast_coords_df</span><span class="p">(</span><span class="n">df</span><span class="p">):</span>
<span class="n">coords</span> <span class="o">=</span> <span class="n">fix_blast_coords</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">sstart</span><span class="o">.</span><span class="n">values</span><span class="p">,</span> <span class="n">df</span><span class="o">.</span><span class="n">send</span><span class="o">.</span><span class="n">values</span><span class="p">,</span> <span class="n">df</span><span class="o">.</span><span class="n">qstart</span><span class="o">.</span><span class="n">values</span><span class="p">,</span> <span class="n">df</span><span class="o">.</span><span class="n">qend</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
<span class="n">df</span><span class="p">[</span><span class="s">&#39;sstart&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">0</span><span class="p">]</span>
<span class="n">df</span><span class="p">[</span><span class="s">&#39;send&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">1</span><span class="p">]</span>
<span class="n">df</span><span class="p">[</span><span class="s">&#39;qstart&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">2</span><span class="p">]</span>
<span class="n">df</span><span class="p">[</span><span class="s">&#39;qend&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">3</span><span class="p">]</span>
<span class="n">df</span><span class="p">[</span><span class="s">&#39;sstrand&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">4</span><span class="p">]</span>
<span class="n">df</span><span class="p">[</span><span class="s">&#39;qstrand&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">5</span><span class="p">]</span></div>
<span class="n">df</span><span class="p">[</span><span class="s1">&#39;sstart&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">0</span><span class="p">]</span>
<span class="n">df</span><span class="p">[</span><span class="s1">&#39;send&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">1</span><span class="p">]</span>
<span class="n">df</span><span class="p">[</span><span class="s1">&#39;qstart&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">2</span><span class="p">]</span>
<span class="n">df</span><span class="p">[</span><span class="s1">&#39;qend&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">3</span><span class="p">]</span>
<span class="n">df</span><span class="p">[</span><span class="s1">&#39;sstrand&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">4</span><span class="p">]</span>
<span class="n">df</span><span class="p">[</span><span class="s1">&#39;qstrand&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span><span class="p">[:,</span><span class="mi">5</span><span class="p">]</span></div>
</pre></div>

</div>
Expand All @@ -128,14 +133,11 @@ <h3>Related Topics</h3>
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Expand All @@ -146,8 +148,8 @@ <h3>Quick search</h3>
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