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| <div class="section" id="module-apache_beam.io.vcfio"> |
| <span id="apache-beam-io-vcfio-module"></span><h1>apache_beam.io.vcfio module<a class="headerlink" href="#module-apache_beam.io.vcfio" title="Permalink to this headline">¶</a></h1> |
| <p>A source for reading from VCF files (version 4.x).</p> |
| <p>The 4.2 spec is available at <a class="reference external" href="https://samtools.github.io/hts-specs/VCFv4.2.pdf">https://samtools.github.io/hts-specs/VCFv4.2.pdf</a>.</p> |
| <dl class="class"> |
| <dt id="apache_beam.io.vcfio.VariantInfo"> |
| <em class="property">class </em><code class="descclassname">apache_beam.io.vcfio.</code><code class="descname">VariantInfo</code><span class="sig-paren">(</span><em>data</em>, <em>field_count</em><span class="sig-paren">)</span><a class="headerlink" href="#apache_beam.io.vcfio.VariantInfo" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.8)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a></p> |
| <p>Create new instance of VariantInfo(data, field_count)</p> |
| <dl class="attribute"> |
| <dt id="apache_beam.io.vcfio.VariantInfo.data"> |
| <code class="descname">data</code><a class="headerlink" href="#apache_beam.io.vcfio.VariantInfo.data" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Alias for field number 0</p> |
| </dd></dl> |
| |
| <dl class="attribute"> |
| <dt id="apache_beam.io.vcfio.VariantInfo.field_count"> |
| <code class="descname">field_count</code><a class="headerlink" href="#apache_beam.io.vcfio.VariantInfo.field_count" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Alias for field number 1</p> |
| </dd></dl> |
| |
| </dd></dl> |
| |
| <dl class="class"> |
| <dt id="apache_beam.io.vcfio.MalformedVcfRecord"> |
| <em class="property">class </em><code class="descclassname">apache_beam.io.vcfio.</code><code class="descname">MalformedVcfRecord</code><span class="sig-paren">(</span><em>file_name</em>, <em>line</em><span class="sig-paren">)</span><a class="headerlink" href="#apache_beam.io.vcfio.MalformedVcfRecord" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.8)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a></p> |
| <p>Create new instance of MalformedVcfRecord(file_name, line)</p> |
| <dl class="attribute"> |
| <dt id="apache_beam.io.vcfio.MalformedVcfRecord.file_name"> |
| <code class="descname">file_name</code><a class="headerlink" href="#apache_beam.io.vcfio.MalformedVcfRecord.file_name" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Alias for field number 0</p> |
| </dd></dl> |
| |
| <dl class="attribute"> |
| <dt id="apache_beam.io.vcfio.MalformedVcfRecord.line"> |
| <code class="descname">line</code><a class="headerlink" href="#apache_beam.io.vcfio.MalformedVcfRecord.line" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Alias for field number 1</p> |
| </dd></dl> |
| |
| </dd></dl> |
| |
| <dl class="class"> |
| <dt id="apache_beam.io.vcfio.Variant"> |
| <em class="property">class </em><code class="descclassname">apache_beam.io.vcfio.</code><code class="descname">Variant</code><span class="sig-paren">(</span><em>reference_name=None</em>, <em>start=None</em>, <em>end=None</em>, <em>reference_bases=None</em>, <em>alternate_bases=None</em>, <em>names=None</em>, <em>quality=None</em>, <em>filters=None</em>, <em>info=None</em>, <em>calls=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/vcfio.html#Variant"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.vcfio.Variant" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.8)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p> |
| <p>A class to store info about a genomic variant.</p> |
| <p>Each object corresponds to a single record in a VCF file.</p> |
| <p>Initialize the <a class="reference internal" href="#apache_beam.io.vcfio.Variant" title="apache_beam.io.vcfio.Variant"><code class="xref py py-class docutils literal notranslate"><span class="pre">Variant</span></code></a> object.</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"><ul class="first last simple"> |
| <li><strong>reference_name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a>) – The reference on which this variant occurs |
| (such as <cite>chr20</cite> or <cite>X</cite>). .</li> |
| <li><strong>start</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a>) – The position at which this variant occurs (0-based). |
| Corresponds to the first base of the string of reference bases.</li> |
| <li><strong>end</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a>) – The end position (0-based) of this variant. Corresponds to the |
| first base after the last base in the reference allele.</li> |
| <li><strong>reference_bases</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a>) – The reference bases for this variant.</li> |
| <li><strong>alternate_bases</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a><em>]</em>) – The bases that appear instead of the |
| reference bases.</li> |
| <li><strong>names</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a><em>]</em>) – Names for the variant, for example a RefSNP ID.</li> |
| <li><strong>quality</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a>) – Phred-scaled quality score (-10log10 prob(call is wrong)) |
| Higher values imply better quality.</li> |
| <li><strong>filters</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a><em>]</em>) – A list of filters (normally quality filters) this |
| variant has failed. <cite>PASS</cite> indicates this variant has passed all |
| filters.</li> |
| <li><strong>info</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.8)"><em>dict</em></a>) – A map of additional variant information. The key is specified |
| in the VCF record and the value is of type <code class="docutils literal notranslate"><span class="pre">VariantInfo</span></code>.</li> |
| <li><strong>calls</strong> (list of <a class="reference internal" href="#apache_beam.io.vcfio.VariantCall" title="apache_beam.io.vcfio.VariantCall"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantCall</span></code></a>) – The variant calls for this variant. |
| Each one represents the determination of genotype with respect to this |
| variant.</li> |
| </ul> |
| </td> |
| </tr> |
| </tbody> |
| </table> |
| </dd></dl> |
| |
| <dl class="class"> |
| <dt id="apache_beam.io.vcfio.VariantCall"> |
| <em class="property">class </em><code class="descclassname">apache_beam.io.vcfio.</code><code class="descname">VariantCall</code><span class="sig-paren">(</span><em>name=None</em>, <em>genotype=None</em>, <em>phaseset=None</em>, <em>info=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/vcfio.html#VariantCall"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.vcfio.VariantCall" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.8)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p> |
| <p>A class to store info about a variant call.</p> |
| <p>A call represents the determination of genotype with respect to a particular |
| variant. It may include associated information such as quality and phasing.</p> |
| <p>Initialize the <a class="reference internal" href="#apache_beam.io.vcfio.VariantCall" title="apache_beam.io.vcfio.VariantCall"><code class="xref py py-class docutils literal notranslate"><span class="pre">VariantCall</span></code></a> object.</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"><ul class="first last simple"> |
| <li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a>) – The name of the call.</li> |
| <li><strong>genotype</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a><em>]</em>) – The genotype of this variant call as specified by |
| the VCF schema. The values are either <cite>0</cite> representing the reference, |
| or a 1-based index into alternate bases. Ordering is only important if |
| <cite>phaseset</cite> is present. If a genotype is not called (that is, a <cite>.</cite> is |
| present in the GT string), -1 is used</li> |
| <li><strong>phaseset</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a>) – If this field is present, this variant call’s genotype |
| ordering implies the phase of the bases and is consistent with any other |
| variant calls in the same reference sequence which have the same |
| phaseset value. If the genotype data was phased but no phase set was |
| specified, this field will be set to <cite>*</cite>.</li> |
| <li><strong>info</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.8)"><em>dict</em></a>) – A map of additional variant call information. The key is |
| specified in the VCF record and the type of the value is specified by |
| the VCF header FORMAT.</li> |
| </ul> |
| </td> |
| </tr> |
| </tbody> |
| </table> |
| </dd></dl> |
| |
| <dl class="class"> |
| <dt id="apache_beam.io.vcfio.ReadFromVcf"> |
| <em class="property">class </em><code class="descclassname">apache_beam.io.vcfio.</code><code class="descname">ReadFromVcf</code><span class="sig-paren">(</span><em>file_pattern=None</em>, <em>compression_type='auto'</em>, <em>validate=True</em>, <em>allow_malformed_records=False</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/vcfio.html#ReadFromVcf"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.vcfio.ReadFromVcf" title="Permalink to this definition">¶</a></dt> |
| <dd><p>Bases: <a class="reference internal" href="apache_beam.transforms.ptransform.html#apache_beam.transforms.ptransform.PTransform" title="apache_beam.transforms.ptransform.PTransform"><code class="xref py py-class docutils literal notranslate"><span class="pre">apache_beam.transforms.ptransform.PTransform</span></code></a></p> |
| <p>A <a class="reference internal" href="apache_beam.transforms.ptransform.html#apache_beam.transforms.ptransform.PTransform" title="apache_beam.transforms.ptransform.PTransform"><code class="xref py py-class docutils literal notranslate"><span class="pre">PTransform</span></code></a> for reading VCF |
| files.</p> |
| <p>Parses VCF files (version 4) using PyVCF library. If file_pattern specifies |
| multiple files, then the header from each file is used separately to parse |
| the content. However, the output will be a PCollection of |
| <a class="reference internal" href="#apache_beam.io.vcfio.Variant" title="apache_beam.io.vcfio.Variant"><code class="xref py py-class docutils literal notranslate"><span class="pre">Variant</span></code></a> (or <a class="reference internal" href="#apache_beam.io.vcfio.MalformedVcfRecord" title="apache_beam.io.vcfio.MalformedVcfRecord"><code class="xref py py-class docutils literal notranslate"><span class="pre">MalformedVcfRecord</span></code></a> for failed reads) objects.</p> |
| <p>Initialize the <a class="reference internal" href="#apache_beam.io.vcfio.ReadFromVcf" title="apache_beam.io.vcfio.ReadFromVcf"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReadFromVcf</span></code></a> transform.</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"><ul class="first last simple"> |
| <li><strong>file_pattern</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a>) – The file path to read from either as a single file or |
| a glob pattern.</li> |
| <li><strong>compression_type</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a>) – Used to handle compressed input files. |
| Typical value is <a class="reference internal" href="apache_beam.io.filesystem.html#apache_beam.io.filesystem.CompressionTypes.AUTO" title="apache_beam.io.filesystem.CompressionTypes.AUTO"><code class="xref py py-attr docutils literal notranslate"><span class="pre">CompressionTypes.AUTO</span></code></a>, in which case the |
| underlying file_path’s extension will be used to detect the compression.</li> |
| <li><strong>validate</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.8)"><em>bool</em></a>) – flag to verify that the files exist during the pipeline |
| creation time.</li> |
| <li><strong>allow_malformed_records</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.8)"><em>bool</em></a>) – determines if failed VCF |
| record reads will be tolerated. Failed record reads will result in a |
| <a class="reference internal" href="#apache_beam.io.vcfio.MalformedVcfRecord" title="apache_beam.io.vcfio.MalformedVcfRecord"><code class="xref py py-class docutils literal notranslate"><span class="pre">MalformedVcfRecord</span></code></a> being returned from the read of the record |
| rather than a <a class="reference internal" href="#apache_beam.io.vcfio.Variant" title="apache_beam.io.vcfio.Variant"><code class="xref py py-class docutils literal notranslate"><span class="pre">Variant</span></code></a>.</li> |
| </ul> |
| </td> |
| </tr> |
| </tbody> |
| </table> |
| <dl class="method"> |
| <dt id="apache_beam.io.vcfio.ReadFromVcf.expand"> |
| <code class="descname">expand</code><span class="sig-paren">(</span><em>pvalue</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/vcfio.html#ReadFromVcf.expand"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.vcfio.ReadFromVcf.expand" title="Permalink to this definition">¶</a></dt> |
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