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<a href="BioSQL-module.html">Package BioSQL</a> ::
<a href="BioSQL.BioSeqDatabase-module.html">Module BioSeqDatabase</a> ::
Class BioSeqDatabase
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class BioSeqDatabase</h1><p class="nomargin-top"><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase">source code</a></span></p>
<p>Represents a namespace (sub-database) within the BioSQL database.</p>
<p>i.e. One row in the biodatabase table, and all all rows in the
bioentry table associated with it.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td align="left"><span class="table-header">Instance Methods</span></td>
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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">adaptor</span>,
<span class="summary-sig-arg">name</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.__init__">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></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.__repr__">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.BioSeqDatabase.BioSeqDatabase-class.html#get_Seq_by_id" class="summary-sig-name">get_Seq_by_id</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>)</span><br />
Gets a DBSeqRecord object by its name</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_Seq_by_id">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.BioSeqDatabase.BioSeqDatabase-class.html#get_Seq_by_acc" class="summary-sig-name">get_Seq_by_acc</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>)</span><br />
Gets a DBSeqRecord object by accession number</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_Seq_by_acc">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.BioSeqDatabase.BioSeqDatabase-class.html#get_Seq_by_ver" class="summary-sig-name">get_Seq_by_ver</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>)</span><br />
Gets a DBSeqRecord object by version number</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_Seq_by_ver">source code</a></span>
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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.BioSeqDatabase.BioSeqDatabase-class.html#get_Seqs_by_acc" class="summary-sig-name">get_Seqs_by_acc</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>)</span><br />
Gets a list of DBSeqRecord objects by accession number</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_Seqs_by_acc">source code</a></span>
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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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<td><span class="summary-sig"><a href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#get_all_primary_ids" class="summary-sig-name">get_all_primary_ids</a>(<span class="summary-sig-arg">self</span>)</span><br />
All the primary_ids of the sequences in the database (OBSOLETE).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_all_primary_ids">source code</a></span>
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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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<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">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.__getitem__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__delitem__"></a><span class="summary-sig-name">__delitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span><br />
Remove an entry and all its annotation.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.__delitem__">source code</a></span>
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<span class="summary-type"> </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 />
Number of records in this namespace (sub database).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.__len__">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__contains__"></a><span class="summary-sig-name">__contains__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span><br />
Check if a primary (internal) id is this namespace (sub database).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.__contains__">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 name="__iter__"></a><span class="summary-sig-name">__iter__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over ids (which may not be meaningful outside this database).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.__iter__">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 name="iterkeys"></a><span class="summary-sig-name">iterkeys</span>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over ids (which may not be meaningful outside this database).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.iterkeys">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="itervalues"></a><span class="summary-sig-name">itervalues</span>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over DBSeqRecord objects in the namespace (sub database).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.itervalues">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="iteritems"></a><span class="summary-sig-name">iteritems</span>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over (id, DBSeqRecord) for the namespace (sub database).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.iteritems">source code</a></span>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="keys"></a><span class="summary-sig-name">keys</span>(<span class="summary-sig-arg">self</span>)</span><br />
List of ids which may not be meaningful outside this database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.keys">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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<td><span class="summary-sig"><a name="values"></a><span class="summary-sig-name">values</span>(<span class="summary-sig-arg">self</span>)</span><br />
List of DBSeqRecord objects in the namespace (sub database).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.values">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 name="items"></a><span class="summary-sig-name">items</span>(<span class="summary-sig-arg">self</span>)</span><br />
List of (id, DBSeqRecord) for the namespace (sub database).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.items">source code</a></span>
</td>
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<td><span class="summary-sig"><a name="lookup"></a><span class="summary-sig-name">lookup</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">**kwargs</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.lookup">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.BioSeqDatabase.BioSeqDatabase-class.html#get_Seq_by_primary_id" class="summary-sig-name">get_Seq_by_primary_id</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">seqid</span>)</span><br />
Get a DBSeqRecord by the primary (internal) id (OBSOLETE).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_Seq_by_primary_id">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<tr>
<td><span class="summary-sig"><a href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#load" class="summary-sig-name">load</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record_iterator</span>,
<span class="summary-sig-arg">fetch_NCBI_taxonomy</span>=<span class="summary-sig-default">False</span>)</span><br />
Load a set of SeqRecords into the BioSQL database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.load">source code</a></span>
</td>
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<!-- ==================== METHOD DETAILS ==================== -->
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<td align="left"><span class="table-header">Method Details</span></td>
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<a name="get_Seq_by_id"></a>
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<table class="details" border="1" cellpadding="3"
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_Seq_by_id</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_Seq_by_id">source code</a></span>
</td>
</tr></table>
<p>Gets a DBSeqRecord object by its name</p>
<p>Example: seq_rec = db.get_Seq_by_id('ROA1_HUMAN')</p>
<p>The name of this method is misleading since it returns a DBSeqRecord
rather than a DBSeq ojbect, and presumably was to mirror BioPerl.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_Seq_by_acc"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_Seq_by_acc</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_Seq_by_acc">source code</a></span>
</td>
</tr></table>
<p>Gets a DBSeqRecord object by accession number</p>
<p>Example: seq_rec = db.get_Seq_by_acc('X77802')</p>
<p>The name of this method is misleading since it returns a DBSeqRecord
rather than a DBSeq ojbect, and presumably was to mirror BioPerl.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_Seq_by_ver"></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">get_Seq_by_ver</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_Seq_by_ver">source code</a></span>
</td>
</tr></table>
<p>Gets a DBSeqRecord object by version number</p>
<p>Example: seq_rec = db.get_Seq_by_ver('X77802.1')</p>
<p>The name of this method is misleading since it returns a DBSeqRecord
rather than a DBSeq ojbect, and presumably was to mirror BioPerl.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_Seqs_by_acc"></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">get_Seqs_by_acc</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_Seqs_by_acc">source code</a></span>
</td>
</tr></table>
<p>Gets a list of DBSeqRecord objects by accession number</p>
<p>Example: seq_recs = db.get_Seq_by_acc('X77802')</p>
<p>The name of this method is misleading since it returns a list of
DBSeqRecord objects rather than a list of DBSeq ojbects, and presumably
was to mirror BioPerl.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_all_primary_ids"></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">get_all_primary_ids</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_all_primary_ids">source code</a></span>
</td>
</tr></table>
<p>All the primary_ids of the sequences in the database (OBSOLETE).</p>
<p>These maybe ids (display style) or accession numbers or something else
completely different - they *are not* meaningful outside of this database
implementation.</p>
<p>Please use .keys() instead of .get_all_primary_ids()</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_Seq_by_primary_id"></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">get_Seq_by_primary_id</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">seqid</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.get_Seq_by_primary_id">source code</a></span>
</td>
</tr></table>
<p>Get a DBSeqRecord by the primary (internal) id (OBSOLETE).</p>
<p>Rather than db.get_Seq_by_primary_id(my_id) use db[my_id]</p>
<p>The name of this method is misleading since it returns a DBSeqRecord
rather than a DBSeq ojbect, and presumably was to mirror BioPerl.</p>
<dl class="fields">
</dl>
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<a name="load"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">load</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">record_iterator</span>,
<span class="sig-arg">fetch_NCBI_taxonomy</span>=<span class="sig-default">False</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#BioSeqDatabase.load">source code</a></span>
</td>
</tr></table>
<p>Load a set of SeqRecords into the BioSQL database.</p>
<p>record_iterator is either a list of SeqRecord objects, or an Iterator
object that returns SeqRecord objects (such as the output from the
Bio.SeqIO.parse() function), which will be used to populate the
database.</p>
<p>fetch_NCBI_taxonomy is boolean flag allowing or preventing connection
to the taxonomic database on the NCBI server (via Bio.Entrez) to fetch a
detailed taxonomy for each SeqRecord.</p>
<p>Example: from Bio import SeqIO count =
db.load(SeqIO.parse(open(filename), format))</p>
<p>Returns the number of records loaded.</p>
<dl class="fields">
</dl>
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