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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqRecord-module.html">Module SeqRecord</a> ::
Class SeqRecord
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SeqRecord</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqRecord-pysrc.html#SeqRecord">source code</a></span></p>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="BioSQL.BioSeq.DBSeqRecord-class.html">BioSQL.BioSeq.DBSeqRecord</a></li> </ul>
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<pre class="literalblock">
A SeqRecord object holds a sequence and information about it.
Main attributes:
id - Identifier such as a locus tag (string)
seq - The sequence itself (Seq object)
Additional attributes:
name - Sequence name, e.g. gene name (string)
description - Additional text (string)
dbxrefs - List of database cross references (list of strings)
features - Any (sub)features defined (list of SeqFeature objects)
annotations - Further information about the whole sequence (dictionary)
Most entries are lists of strings.
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<td><span class="summary-sig"><a href="Bio.SeqRecord.SeqRecord-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"><unknown id></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">name</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"><unknown name></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">description</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"><unknown description></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">dbxrefs</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">features</span>=<span class="summary-sig-default">None</span>)</span><br />
Create a SeqRecord.</td>
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<span class="codelink"><a href="Bio.SeqRecord-pysrc.html#SeqRecord.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="__len__"></a><span class="summary-sig-name">__len__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the length of the sequence.</td>
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<td><span class="summary-sig"><a href="Bio.SeqRecord.SeqRecord-class.html#__nonzero__" class="summary-sig-name">__nonzero__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns True regardless of the length of the sequence.</td>
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<td><span class="summary-sig"><a name="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span><br />
A concise summary of the record for debugging.</td>
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<span class="codelink"><a href="Bio.SeqRecord-pysrc.html#SeqRecord.__repr__">source code</a></span>
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<td><span class="summary-sig"><a name="__str__"></a><span class="summary-sig-name">__str__</span>(<span class="summary-sig-arg">self</span>)</span><br />
A human readable summary of the record and its annotation.</td>
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<span class="codelink"><a href="Bio.SeqRecord-pysrc.html#SeqRecord.__str__">source code</a></span>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">seq</span>,
<span class="sig-arg">id</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"><unknown id></code><code class="variable-quote">'</code></span>,
<span class="sig-arg">name</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"><unknown name></code><code class="variable-quote">'</code></span>,
<span class="sig-arg">description</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"><unknown description></code><code class="variable-quote">'</code></span>,
<span class="sig-arg">dbxrefs</span>=<span class="sig-default">None</span>,
<span class="sig-arg">features</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
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<p>Create a SeqRecord.</p>
<p>Arguments: seq - Sequence, required (Seq object) id -
Sequence identifier, recommended (string) name - Sequence name,
optional (string) description - Sequence description, optional (string)
dbxrefs - Database cross references, optional (list of strings)
features - Any (sub)features, optional (list of SeqFeature
objects)</p>
<p>Note that while an id is optional, we strongly recommend you supply a
unique id string for each record. This is especially important if you
wish to write your sequences to a file.</p>
<p>You can create a 'blank' SeqRecord object, and then populated the
attributes later. Note that currently the annotations dictionary cannot
be specified when creating the SeqRecord.</p>
<dl class="fields">
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<a name="__nonzero__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__nonzero__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Boolean test operator)</em>
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><span class="codelink"><a href="Bio.SeqRecord-pysrc.html#SeqRecord.__nonzero__">source code</a></span>
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<p>Returns True regardless of the length of the sequence.</p>
<p>This behaviour is for backwards compatibility, since until the __len__
method was added, a SeqRecord always evaluated as True.</p>
<p>Note that in comparison, a Seq object will evaluate to False if it has
a zero length sequence.</p>
<p>WARNING: The SeqRecord may in future evaluate to False when its
sequence is of zero length (in order to better match the Seq object
behaviour)!</p>
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