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<title>BAM — baseq 0.01 documentation</title>
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<div class="section" id="bam">
<span id="id1"></span><h1>BAM<a class="headerlink" href="#bam" title="Permalink to this headline">¶</a></h1>
<div class="section" id="functions">
<h2>Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>Read bam file, stats the bamfile (reads, mapping ratio…);</li>
<li>Get the depth for a genomic region (and visualization);</li>
<li>Get the reads overlapped with a genomic region;</li>
</ul>
</div>
<div class="section" id="design">
<h2>Design<a class="headerlink" href="#design" title="Permalink to this headline">¶</a></h2>
<p>Most of the function develop based on “samtools”. The version should be >=1.3.0</p>
<ul class="simple">
<li>samtools depth: to get the coverage depth;</li>
<li>samtools view chrN:start-end : to get the overlapped reads;</li>
</ul>
</div>
<div class="section" id="class">
<h2>Class<a class="headerlink" href="#class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="baseq.bam.BAMTYPE">
<em class="property">class </em><code class="descclassname">baseq.bam.</code><code class="descname">BAMTYPE</code><span class="sig-paren">(</span><em>path</em>, <em>bedfile=''</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/bam/bamtype.html#BAMTYPE"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.bam.BAMTYPE" title="Permalink to this definition">¶</a></dt>
<dd><p>BAM File Handler, Based on samtools.
While initiate, it read the path using samtools and will parse the headers.</p>
<dl class="docutils">
<dt>Usage:</dt>
<dd><ul class="first last simple">
<li>Stats on enrichment quality.</li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="baseq.bam.BAMTYPE.get_columns">
<code class="descname">get_columns</code><span class="sig-paren">(</span><em>rows=10000</em>, <em>colIdx=6</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/bam/bamtype.html#BAMTYPE.get_columns"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.bam.BAMTYPE.get_columns" title="Permalink to this definition">¶</a></dt>
<dd><p>Read the bamfile using samtools, get the infors in the column<colIDx> and first <rows> of Rows.
The columns of bam files are:</p>
<ol class="arabic simple">
<li>header</li>
<li>flags</li>
<li>chromosome</li>
<li>start</li>
<li>mapping quality</li>
<li>cigar</li>
</ol>
<p>The colIdx start from 1.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">BAMTYPE</span><span class="p">(</span><span class="n">path</span><span class="p">)</span><span class="o">.</span><span class="n">get_columns</span><span class="p">(</span><span class="mi">1000</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
<span class="c1"># ['chr1', 'chr1', ...]</span>
</pre></div>
</div>
</dd></dl>
<dl class="method">
<dt id="baseq.bam.BAMTYPE.get_reads">
<code class="descname">get_reads</code><span class="sig-paren">(</span><em>chr</em>, <em>start</em>, <em>end</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/bam/bamtype.html#BAMTYPE.get_reads"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.bam.BAMTYPE.get_reads" title="Permalink to this definition">¶</a></dt>
<dd><p>Return The Reads that overlaps with region chrN:start-end.</p>
<ul class="simple">
<li>Skip reads contains “N” cigar.</li>
</ul>
</dd></dl>
<dl class="method">
<dt id="baseq.bam.BAMTYPE.read_counts">
<code class="descname">read_counts</code><span class="sig-paren">(</span><em>chr</em>, <em>star</em>, <em>end</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/bam/bamtype.html#BAMTYPE.read_counts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.bam.BAMTYPE.read_counts" title="Permalink to this definition">¶</a></dt>
<dd><dl class="docutils">
<dt>Todo:</dt>
<dd><ul class="first last simple">
<li>For module TODOs</li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="baseq.bam.BAMTYPE.region_bed_depth">
<code class="descname">region_bed_depth</code><span class="sig-paren">(</span><em>bedfile</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/bam/bamtype.html#BAMTYPE.region_bed_depth"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.bam.BAMTYPE.region_bed_depth" title="Permalink to this definition">¶</a></dt>
<dd><p>The depth of regions in an bed file.</p>
</dd></dl>
<dl class="method">
<dt id="baseq.bam.BAMTYPE.region_depth">
<code class="descname">region_depth</code><span class="sig-paren">(</span><em>chr</em>, <em>start</em>, <em>end</em>, <em>all=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/bam/bamtype.html#BAMTYPE.region_depth"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.bam.BAMTYPE.region_depth" title="Permalink to this definition">¶</a></dt>
<dd><p>Get the depth coverage of bases in the region.
It will suitable for chromesome name like “chr1” and “1”.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>all</strong> – Shall the bases with zero coverge be returned.</td>
</tr>
</tbody>
</table>
<p>Usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>BAMTYPE(path).region_depth("chr1", 1000, 2000, all=True)
`return depth list [0,1,1,1,2,2,2,3,0]`
</pre></div>
</div>
</dd></dl>
<dl class="method">
<dt id="baseq.bam.BAMTYPE.stats_bam">
<code class="descname">stats_bam</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/bam/bamtype.html#BAMTYPE.stats_bam"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.bam.BAMTYPE.stats_bam" title="Permalink to this definition">¶</a></dt>
<dd><p>Read the bampath.stat, if not exists, perform the <cite>samtools flagstat</cite>
The results will be:</p>
<ol class="arabic simple">
<li>self.reads_total</li>
<li>self.reads_mapped</li>
<li>self.mapping_ratio</li>
</ol>
</dd></dl>
<dl class="method">
<dt id="baseq.bam.BAMTYPE.stats_bases">
<code class="descname">stats_bases</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/bam/bamtype.html#BAMTYPE.stats_bases"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.bam.BAMTYPE.stats_bases" title="Permalink to this definition">¶</a></dt>
<dd><p>Stats on the mean match length for the top 100K reads in the bam file</p>
</dd></dl>
<dl class="method">
<dt id="baseq.bam.BAMTYPE.stats_duplicates">
<code class="descname">stats_duplicates</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/bam/bamtype.html#BAMTYPE.stats_duplicates"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.bam.BAMTYPE.stats_duplicates" title="Permalink to this definition">¶</a></dt>
<dd><p>Stats Duplication Rates from the top 1M reads;
The duplication should be reflected in the flag</p>
</dd></dl>
<dl class="method">
<dt id="baseq.bam.BAMTYPE.stats_region_coverage">
<code class="descname">stats_region_coverage</code><span class="sig-paren">(</span><em>numbers=1000</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/bam/bamtype.html#BAMTYPE.stats_region_coverage"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.bam.BAMTYPE.stats_region_coverage" title="Permalink to this definition">¶</a></dt>
<dd><p>Check the enrichment quality.</p>
<ul class="simple">
<li>Require a bedfile while initiating the class</li>
<li>Select <numbers> regions randomly</li>
<li>Use multithread pool to get the coverage depth of the regions</li>
<li>Stats on the ratio of 10X, 30X, 50X and 100X bases</li>
</ul>
<p>Usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">BAMTYPE</span><span class="p">(</span><span class="s2">"sample.bam"</span><span class="p">,</span> <span class="s2">"panel.bed"</span><span class="p">)</span><span class="o">.</span><span class="n">stats_region_coverage</span><span class="p">(</span><span class="mi">1000</span><span class="p">)</span>
<span class="n">The</span> <span class="n">results</span> <span class="n">will</span> <span class="n">be</span> <span class="n">save</span> <span class="ow">in</span> <span class="nb">object</span> <span class="n">properies</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">mean_depth</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">pct_10X</span><span class="o">/..</span>
</pre></div>
</div>
</dd></dl>
</dd></dl>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">BAM</a><ul>
<li><a class="reference internal" href="#functions">Functions</a></li>
<li><a class="reference internal" href="#design">Design</a></li>
<li><a class="reference internal" href="#class">Class</a></li>
</ul>
</li>
</ul>
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<h3>Related Topics</h3>
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<li><a href="index.html">Documentation overview</a><ul>
<li>Previous: <a href="guidance/pandas.html" title="previous chapter">数据框操作</a></li>
<li>Next: <a href="CNV/CNV.html" title="next chapter">CNV Analysis</a></li>
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