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<a href="BioSQL-module.html">Package BioSQL</a> ::
<a href="BioSQL.BioSeq-module.html">Module BioSeq</a> ::
Class DBSeq
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class DBSeq</h1><p class="nomargin-top"><span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.Seq.Seq-class.html">Bio.Seq.Seq</a> --+
|
<strong class="uidshort">DBSeq</strong>
</pre>
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<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeq-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">primary_id</span>,
<span class="summary-sig-arg">adaptor</span>,
<span class="summary-sig-arg">alphabet</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">length</span>)</span><br />
Create a new DBSeq object referring to a BioSQL entry.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.__init__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeq-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the length of the sequence, use len(my_seq).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.__len__">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeq-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">index</span>)</span><br />
Returns a subsequence of single letter, use my_seq[index].</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.__getitem__">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeq-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>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.tostring">source code</a></span>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeq-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="BioSQL.BioSeq-pysrc.html#DBSeq.__str__">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<tr>
<td><span class="summary-sig"><a name="toseq"></a><span class="summary-sig-name">toseq</span>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the full sequence as a Seq object.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.toseq">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeq-class.html#__add__" class="summary-sig-name">__add__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Add another sequence or string to this sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.__add__">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeq-class.html#__radd__" class="summary-sig-name">__radd__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Adding a sequence on the left.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.__radd__">source code</a></span>
</td>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Seq.Seq-class.html">Bio.Seq.Seq</a></code></b>:
<code><a href="Bio.Seq.Seq-class.html#__cmp__">__cmp__</a></code>,
<code><a href="Bio.Seq.Seq-class.html#__contains__">__contains__</a></code>,
<code><a href="Bio.Seq.Seq-class.html#__hash__">__hash__</a></code>,
<code><a href="Bio.Seq.Seq-class.html#__repr__">__repr__</a></code>,
<code><a href="Bio.Seq.Seq-class.html#back_transcribe">back_transcribe</a></code>,
<code><a href="Bio.Seq.Seq-class.html#complement">complement</a></code>,
<code><a href="Bio.Seq.Seq-class.html#count">count</a></code>,
<code><a href="Bio.Seq.Seq-class.html#endswith">endswith</a></code>,
<code><a href="Bio.Seq.Seq-class.html#find">find</a></code>,
<code><a href="Bio.Seq.Seq-class.html#lower">lower</a></code>,
<code><a href="Bio.Seq.Seq-class.html#lstrip">lstrip</a></code>,
<code><a href="Bio.Seq.Seq-class.html#reverse_complement">reverse_complement</a></code>,
<code><a href="Bio.Seq.Seq-class.html#rfind">rfind</a></code>,
<code><a href="Bio.Seq.Seq-class.html#rsplit">rsplit</a></code>,
<code><a href="Bio.Seq.Seq-class.html#rstrip">rstrip</a></code>,
<code><a href="Bio.Seq.Seq-class.html#split">split</a></code>,
<code><a href="Bio.Seq.Seq-class.html#startswith">startswith</a></code>,
<code><a href="Bio.Seq.Seq-class.html#strip">strip</a></code>,
<code><a href="Bio.Seq.Seq-class.html#tomutable">tomutable</a></code>,
<code><a href="Bio.Seq.Seq-class.html#transcribe">transcribe</a></code>,
<code><a href="Bio.Seq.Seq-class.html#translate">translate</a></code>,
<code><a href="Bio.Seq.Seq-class.html#ungap">ungap</a></code>,
<code><a href="Bio.Seq.Seq-class.html#upper">upper</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Seq.Seq-class.html">Bio.Seq.Seq</a></code></b> (private):
<code><a href="Bio.Seq.Seq-class.html#_get_seq_str_and_check_alphabet" onclick="show_private();">_get_seq_str_and_check_alphabet</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>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
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<!-- ==================== PROPERTIES ==================== -->
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<td align="left"><span class="table-header">Properties</span></td>
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class="privatelink" onclick="toggle_private();"
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<span class="summary-type"> </span>
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<a href="BioSQL.BioSeq.DBSeq-class.html#data" class="summary-name">data</a><br />
Sequence as string (DEPRECATED)
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
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<!-- ==================== METHOD DETAILS ==================== -->
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<a name="__init__"></a>
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">primary_id</span>,
<span class="sig-arg">adaptor</span>,
<span class="sig-arg">alphabet</span>,
<span class="sig-arg">start</span>,
<span class="sig-arg">length</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.__init__">source code</a></span>
</td>
</tr></table>
<p>Create a new DBSeq object referring to a BioSQL entry.</p>
<p>You wouldn't normally create a DBSeq object yourself, this is done for
you when retreiving a DBSeqRecord object from the database.</p>
<dl class="fields">
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="__len__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__len__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Length operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.__len__">source code</a></span>
</td>
</tr></table>
<p>Returns the length of the sequence, use len(my_seq).</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Seq.Seq-class.html#__len__">Bio.Seq.Seq.__len__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__getitem__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">index</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.__getitem__">source code</a></span>
</td>
</tr></table>
<p>Returns a subsequence of single letter, use my_seq[index].</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Seq.Seq-class.html#__getitem__">Bio.Seq.Seq.__getitem__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="tostring"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<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="BioSQL.BioSeq-pysrc.html#DBSeq.tostring">source code</a></span>
</td>
</tr></table>
<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>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Seq.Seq-class.html#tostring">Bio.Seq.Seq.tostring</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__str__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<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="BioSQL.BioSeq-pysrc.html#DBSeq.__str__">source code</a></span>
</td>
</tr></table>
<p>Returns the full sequence as a python string.</p>
<dl class="fields">
<dt>Overrides:
object.__str__
</dt>
</dl>
</td></tr></table>
</div>
<a name="__add__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__add__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">other</span>)</span>
<br /><em class="fname">(Addition operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.__add__">source code</a></span>
</td>
</tr></table>
<p>Add another sequence or string to this sequence.</p>
<p>If adding a string to a Seq, the alphabet is preserved:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Seq <span class="py-keyword">import</span> Seq
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Alphabet <span class="py-keyword">import</span> generic_protein
<span class="py-prompt">>>> </span>Seq(<span class="py-string">"MELKI"</span>, generic_protein) + <span class="py-string">"LV"</span>
<span class="py-output">Seq('MELKILV', ProteinAlphabet())</span></pre>
<p>When adding two Seq (like) objects, the alphabets are important.
Consider this example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Seq <span class="py-keyword">import</span> Seq
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Alphabet.IUPAC <span class="py-keyword">import</span> unambiguous_dna, ambiguous_dna
<span class="py-prompt">>>> </span>unamb_dna_seq = Seq(<span class="py-string">"ACGT"</span>, unambiguous_dna)
<span class="py-prompt">>>> </span>ambig_dna_seq = Seq(<span class="py-string">"ACRGT"</span>, ambiguous_dna)
<span class="py-prompt">>>> </span>unamb_dna_seq
<span class="py-output">Seq('ACGT', IUPACUnambiguousDNA())</span>
<span class="py-output"></span><span class="py-prompt">>>> </span>ambig_dna_seq
<span class="py-output">Seq('ACRGT', IUPACAmbiguousDNA())</span></pre>
<p>If we add the ambiguous and unambiguous IUPAC DNA alphabets, we get
the more general ambiguous IUPAC DNA alphabet:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>unamb_dna_seq + ambig_dna_seq
<span class="py-output">Seq('ACGTACRGT', IUPACAmbiguousDNA())</span></pre>
<p>However, if the default generic alphabet is included, the result is a
generic alphabet:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>Seq(<span class="py-string">""</span>) + ambig_dna_seq
<span class="py-output">Seq('ACRGT', Alphabet())</span></pre>
<p>You can't add RNA and DNA sequences:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Alphabet <span class="py-keyword">import</span> generic_dna, generic_rna
<span class="py-prompt">>>> </span>Seq(<span class="py-string">"ACGT"</span>, generic_dna) + Seq(<span class="py-string">"ACGU"</span>, generic_rna)
<span class="py-except">Traceback (most recent call last):</span>
<span class="py-except"> ...</span>
<span class="py-except">TypeError: Incompatible alphabets DNAAlphabet() and RNAAlphabet()</span></pre>
<p>You can't add nucleotide and protein sequences:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Alphabet <span class="py-keyword">import</span> generic_dna, generic_protein
<span class="py-prompt">>>> </span>Seq(<span class="py-string">"ACGT"</span>, generic_dna) + Seq(<span class="py-string">"MELKI"</span>, generic_protein)
<span class="py-except">Traceback (most recent call last):</span>
<span class="py-except"> ...</span>
<span class="py-except">TypeError: Incompatible alphabets DNAAlphabet() and ProteinAlphabet()</span></pre>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Seq.Seq-class.html#__add__">Bio.Seq.Seq.__add__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__radd__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__radd__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">other</span>)</span>
<br /><em class="fname">(Right-side addition operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeq.__radd__">source code</a></span>
</td>
</tr></table>
<p>Adding a sequence on the left.</p>
<p>If adding a string to a Seq, the alphabet is preserved:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Seq <span class="py-keyword">import</span> Seq
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Alphabet <span class="py-keyword">import</span> generic_protein
<span class="py-prompt">>>> </span><span class="py-string">"LV"</span> + Seq(<span class="py-string">"MELKI"</span>, generic_protein)
<span class="py-output">Seq('LVMELKI', ProteinAlphabet())</span></pre>
<p>Adding two Seq (like) objects is handled via the __add__ method.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Seq.Seq-class.html#__radd__">Bio.Seq.Seq.__radd__</a>
<dd><em class="note">(inherited documentation)</em></dd>
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<p>Sequence as string (DEPRECATED)</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeq-class.html#tostring" class="summary-sig-name">tostring</a>(<span class="summary-sig-arg">self</span>)</span>
- Returns the full sequence as a python string.
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