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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Seq-module.html">Module Seq</a> ::
Class Seq
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Seq</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Seq-pysrc.html#Seq">source code</a></span></p>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="BioSQL.BioSeq.DBSeq-class.html">BioSQL.BioSeq.DBSeq</a></li> </ul>
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<td><span class="summary-sig"><a name="__add__"></a><span class="summary-sig-name">__add__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span></td>
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<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.__add__">source code</a></span>
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<td><span class="summary-sig"><a name="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">index</span>)</span></td>
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<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.__getitem__">source code</a></span>
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<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">data</span>,
<span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">Alphabet()</span>)</span></td>
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<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.__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></td>
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<span class="summary-type">translation table</span>
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<td><span class="summary-sig"><a href="Bio.Seq.Seq-class.html#__maketrans" class="summary-sig-name" onclick="show_private();">__maketrans</a>(<span class="summary-sig-arg">Seq</span>,
<span class="summary-sig-arg">alphabet</span>)</span><br />
Return a translation table for use with complement() and
reverse_complement().</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.__maketrans">source code</a></span>
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<td><span class="summary-sig"><a name="__radd__"></a><span class="summary-sig-name">__radd__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span></td>
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<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.__radd__">source code</a></span>
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<span class="summary-type"> </span>
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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 />
Returns a (truncated) representation of the sequence for debugging.</td>
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<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.__repr__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Seq.Seq-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the full sequence as a python string.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.__str__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Seq.Seq-class.html#complement" class="summary-sig-name">complement</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the complement sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.complement">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Seq.Seq-class.html#count" class="summary-sig-name">count</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sub</span>,
<span class="summary-sig-arg">start</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">end</span>=<span class="summary-sig-default">None</span>)</span><br />
Count method, like that of a python string.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.count">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Seq.Seq-class.html#reverse_complement" class="summary-sig-name">reverse_complement</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the reverse complement sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.reverse_complement">source code</a></span>
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<td><span class="summary-sig"><a name="tomutable"></a><span class="summary-sig-name">tomutable</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.tomutable">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Seq.Seq-class.html#tostring" class="summary-sig-name">tostring</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the full sequence as a python string.</td>
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<span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.tostring">source code</a></span>
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<a name="__maketrans"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__maketrans</span>(<span class="sig-arg">Seq</span>,
<span class="sig-arg">alphabet</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.__maketrans">source code</a></span>
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<p>Return a translation table for use with complement() and
reverse_complement().</p>
<p>Compatible with lower case and upper case sequences.</p>
<p>alphabet is a dictionary as implement in Data.IUPACData</p>
<p>For internal use only.</p>
<dl class="fields">
<dt>Returns: translation table</dt>
</dl>
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<a name="__str__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.__str__">source code</a></span>
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<p>Returns the full sequence as a python string.</p>
<p>Note that Biopython 1.44 and earlier would give a truncated version of
repr(my_seq) for str(my_seq). If you are writing code which need to be
backwards compatible with old Biopython, you should continue to use
my_seq.tostring() rather than str(my_seq)</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">complement</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.complement">source code</a></span>
</td>
</tr></table>
<p>Returns the complement sequence. New Seq object.</p>
<dl class="fields">
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">count</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">sub</span>,
<span class="sig-arg">start</span>=<span class="sig-default">None</span>,
<span class="sig-arg">end</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.count">source code</a></span>
</td>
</tr></table>
<p>Count method, like that of a python string.</p>
<p>Return an integer, the number of occurrences of substring argument sub
in the (sub)sequence given by [start:end]. Optional arguments start and
end are interpreted as in slice notation.</p>
<p>sub - a string or another Seq object to look for start - optional
integer, slice start end - optional integer, slice end</p>
<p>e.g. from Bio.Seq import Seq my_seq = Seq("AAAATGA") print
my_seq.count("A") print my_seq.count("ATG") print
my_seq.count(Seq("AT")) print my_seq.count("AT", 2,
-1)</p>
<dl class="fields">
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">reverse_complement</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.reverse_complement">source code</a></span>
</td>
</tr></table>
<p>Returns the reverse complement sequence. New Seq object.</p>
<dl class="fields">
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">tostring</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Seq-pysrc.html#Seq.tostring">source code</a></span>
</td>
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<p>Returns the full sequence as a python string.</p>
<p>Although not formally deprecated, you are now encouraged to use
str(my_seq) instead of my_seq.tostring().</p>
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