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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqIO-module.html">Package SeqIO</a> ::
<a href="Bio.SeqIO.QualityIO-module.html">Module QualityIO</a> ::
Class FastqPhredWriter
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class FastqPhredWriter</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqIO.QualityIO-pysrc.html#FastqPhredWriter">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html">Interfaces.SequenceWriter</a> --+
|
<a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html">Interfaces.SequentialSequenceWriter</a> --+
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<strong class="uidshort">FastqPhredWriter</strong>
</pre>
<hr />
<p>Class to write standard FASTQ format files (using PHRED quality
scores).</p>
<p>Although you can use this class directly, you are strongly encouraged
to use the Bio.SeqIO.write() function instead via the format name
"fastq" or the alias "fastq-sanger". For example,
this code reads in a standard Sanger style FASTQ file (using PHRED
scores) and re-saves it as another Sanger style FASTQ file:</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>record_iterator = SeqIO.parse(open(<span class="py-string">"Quality/example.fastq"</span>), <span class="py-string">"fastq"</span>)
<span class="py-prompt">>>> </span>out_handle = open(<span class="py-string">"Quality/temp.fastq"</span>, <span class="py-string">"w"</span>)
<span class="py-prompt">>>> </span>SeqIO.write(record_iterator, out_handle, <span class="py-string">"fastq"</span>)
<span class="py-output">3</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>out_handle.close()</pre>
<p>You might want to do this if the original file included extra line
breaks, which while valid may not be supported by all tools. The output
file from Biopython will have each sequence on a single line, and each
quality string on a single line (which is considered desirable for
maximum compatibility).</p>
<p>In this next example, an old style Solexa/Illumina FASTQ file (using
Solexa quality scores) is converted into a standard Sanger style FASTQ
file using PHRED qualities:</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>record_iterator = SeqIO.parse(open(<span class="py-string">"Quality/solexa_example.fastq"</span>), <span class="py-string">"fastq-solexa"</span>)
<span class="py-prompt">>>> </span>out_handle = open(<span class="py-string">"Quality/temp.fastq"</span>, <span class="py-string">"w"</span>)
<span class="py-prompt">>>> </span>SeqIO.write(record_iterator, out_handle, <span class="py-string">"fastq"</span>)
<span class="py-output">5</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>out_handle.close()</pre>
<p>This code is also called if you use the .format("fastq")
method of a SeqRecord, or .format("fastq-sanger") if you prefer
that alias.</p>
<p>Note that Sanger FASTQ files have an upper limit of PHRED quality 93,
which is encoded as ASCII 126, the tilde. If your quality scores are
truncated to fit, a warning is issued.</p>
<p>P.S. To avoid cluttering up your working directory, you can delete
this temporary file now:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">import</span> os
<span class="py-prompt">>>> </span>os.remove(<span class="py-string">"Quality/temp.fastq"</span>)</pre>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SeqIO.QualityIO.FastqPhredWriter-class.html#write_record" class="summary-sig-name">write_record</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>)</span><br />
Write a single FASTQ record to the file.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SeqIO.QualityIO-pysrc.html#FastqPhredWriter.write_record">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html">Interfaces.SequentialSequenceWriter</a></code></b>:
<code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#__init__">__init__</a></code>,
<code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_file">write_file</a></code>,
<code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_footer">write_footer</a></code>,
<code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_header">write_header</a></code>,
<code><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_records">write_records</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html">Interfaces.SequenceWriter</a></code></b>:
<code><a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html#clean">clean</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html">Interfaces.SequenceWriter</a></code></b> (private):
<code><a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html#_get_seq_string" onclick="show_private();">_get_seq_string</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<a name="write_record"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">write_record</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">record</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SeqIO.QualityIO-pysrc.html#FastqPhredWriter.write_record">source code</a></span>
</td>
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<p>Write a single FASTQ record to the file.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_record">Interfaces.SequentialSequenceWriter.write_record</a>
</dt>
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