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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqIO-module.html">Package SeqIO</a> ::
Module PhdIO
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<h1 class="epydoc">Module PhdIO</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqIO.PhdIO-pysrc.html">source code</a></span></p>
<p>Bio.SeqIO support for the "phd" file format.</p>
<p>PHD files are output by PHRED and used by PHRAP and CONSED.</p>
<p>You are expected to use this module via the Bio.SeqIO functions, under
the format name "phd". See also the underlying
Bio.Sequencing.Phd module.</p>
<p>For example, using Bio.SeqIO we can read in one of the example PHRED
files from the Biopython unit tests:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio <span class="py-keyword">import</span> SeqIO
<span class="py-prompt">>>> </span><span class="py-keyword">for</span> record <span class="py-keyword">in</span> SeqIO.parse(open(<span class="py-string">"Phd/phd1"</span>), <span class="py-string">"phd"</span>):
<span class="py-more">... </span> <span class="py-keyword">print</span> record.id
<span class="py-more">... </span> <span class="py-keyword">print</span> record.seq[:10], <span class="py-string">"..."</span>
<span class="py-more">... </span> <span class="py-keyword">print</span> record.letter_annotations[<span class="py-string">"phred_quality"</span>][:10], <span class="py-string">"..."</span>
<span class="py-output">34_222_(80-A03-19).b.ab1</span>
<span class="py-output">ctccgtcgga ...</span>
<span class="py-output">[9, 9, 10, 19, 22, 37, 28, 28, 24, 22] ...</span>
<span class="py-output">425_103_(81-A03-19).g.ab1</span>
<span class="py-output">cgggatccca ...</span>
<span class="py-output">[14, 17, 22, 10, 10, 10, 15, 8, 8, 9] ...</span>
<span class="py-output">425_7_(71-A03-19).b.ab1</span>
<span class="py-output">acataaatca ...</span>
<span class="py-output">[10, 10, 10, 10, 8, 8, 6, 6, 6, 6] ...</span></pre>
<p>Since PHRED files contain quality scores, you can save them as FASTQ
or as QUAL files, for example using Bio.SeqIO.write(...), or simply with
the format method of the SeqRecord object:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">print</span> record[:50].format(<span class="py-string">"fastq"</span>)
<span class="py-output">@425_7_(71-A03-19).b.ab1</span>
<span class="py-output">acataaatcaaattactnaccaacacacaaaccngtctcgcgtagtggag</span>
<span class="py-output">+</span>
<span class="py-output">++++))'''')(''')$!$''')''''(+.''$!$))))+)))'''''''</span>
<span class="py-output"><BLANKLINE></span></pre>
<p>Or,</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">print</span> record[:50].format(<span class="py-string">"qual"</span>)
<span class="py-output">>425_7_(71-A03-19).b.ab1</span>
<span class="py-output">10 10 10 10 8 8 6 6 6 6 8 7 6 6 6 8 3 0 3 6 6 6 8 6 6 6 6 7</span>
<span class="py-output">10 13 6 6 3 0 3 8 8 8 8 10 8 8 8 6 6 6 6 6 6 6</span>
<span class="py-output"><BLANKLINE></span></pre>
<p>Note these examples only show the first 50 bases to keep the output
short.</p>
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<span class="summary-type"> </span>
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<a href="Bio.SeqIO.PhdIO.PhdWriter-class.html" class="summary-name">PhdWriter</a><br />
Class to write Phd format files
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<td><span class="summary-sig"><a href="Bio.SeqIO.PhdIO-module.html#PhdIterator" class="summary-sig-name">PhdIterator</a>(<span class="summary-sig-arg">handle</span>)</span><br />
Returns SeqRecord objects from a PHD file.</td>
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<span class="codelink"><a href="Bio.SeqIO.PhdIO-pysrc.html#PhdIterator">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SeqIO.PhdIO-module.html#_test" class="summary-sig-name" onclick="show_private();">_test</a>()</span><br />
Run the Bio.SeqIO.PhdIO module's doctests.</td>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.SeqIO'"><code class="variable-quote">'</code><code class="variable-string">Bio.SeqIO</code><code class="variable-quote">'</code></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">PhdIterator</span>(<span class="sig-arg">handle</span>)</span>
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<p>Returns SeqRecord objects from a PHD file.</p>
<p>This uses the Bio.Sequencing.Phd module to do the hard work.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_test</span>()</span>
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><span class="codelink"><a href="Bio.SeqIO.PhdIO-pysrc.html#_test">source code</a></span>
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<p>Run the Bio.SeqIO.PhdIO module's doctests.</p>
<p>This will try and locate the unit tests directory, and run the
doctests from there in order that the relative paths used in the examples
work.</p>
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