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<a href="BioSQL-module.html">Package BioSQL</a> ::
<a href="BioSQL.Loader-module.html">Module Loader</a> ::
Class DatabaseLoader
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class DatabaseLoader</h1><p class="nomargin-top"><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader">source code</a></span></p>
<p>Load a database with biopython objects.</p>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">adaptor</span>,
<span class="summary-sig-arg">dbid</span>)</span><br />
Initialize with connection information for the database.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="load_seqrecord"></a><span class="summary-sig-name">load_seqrecord</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>)</span><br />
Load a Biopython SeqRecord into the database.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader.load_seqrecord">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_get_ontology_id" class="summary-sig-name" onclick="show_private();">_get_ontology_id</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">definition</span>=<span class="summary-sig-default">None</span>)</span><br />
Returns the identifier for the named ontology.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_ontology_id">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_get_term_id" class="summary-sig-name" onclick="show_private();">_get_term_id</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">ontology_id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">definition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">identifier</span>=<span class="summary-sig-default">None</span>)</span><br />
Get the id that corresponds to a term.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_term_id">source code</a></span>
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<td><span class="summary-sig"><a name="_add_dbxref"></a><span class="summary-sig-name">_add_dbxref</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbname</span>,
<span class="summary-sig-arg">accession</span>,
<span class="summary-sig-arg">version</span>)</span><br />
Insert a dbxref and return its id.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._add_dbxref">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_get_taxon_id" class="summary-sig-name" onclick="show_private();">_get_taxon_id</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>)</span><br />
Get the taxon id for this record.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_taxon_id">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_bioentry_table" class="summary-sig-name" onclick="show_private();">_load_bioentry_table</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>)</span><br />
Fill the bioentry table with sequence information.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_bioentry_table">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_bioentry_date" class="summary-sig-name" onclick="show_private();">_load_bioentry_date</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>,
<span class="summary-sig-arg">bioentry_id</span>)</span><br />
Add the effective date of the entry into the database.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_bioentry_date">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_biosequence" class="summary-sig-name" onclick="show_private();">_load_biosequence</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>,
<span class="summary-sig-arg">bioentry_id</span>)</span><br />
Record a SeqRecord's sequence and alphabet in the database.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_biosequence">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_comment" class="summary-sig-name" onclick="show_private();">_load_comment</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>,
<span class="summary-sig-arg">bioentry_id</span>)</span><br />
Record a SeqRecord's annotated comment in the database.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_comment">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_annotations" class="summary-sig-name" onclick="show_private();">_load_annotations</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>,
<span class="summary-sig-arg">bioentry_id</span>)</span><br />
Record a SeqRecord's misc annotations in the database.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_annotations">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_reference" class="summary-sig-name" onclick="show_private();">_load_reference</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">reference</span>,
<span class="summary-sig-arg">rank</span>,
<span class="summary-sig-arg">bioentry_id</span>)</span><br />
Record a SeqRecord's annotated references in the database.</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_reference">source code</a></span>
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<td><span class="summary-sig"><a name="_load_seqfeature"></a><span class="summary-sig-name">_load_seqfeature</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">feature</span>,
<span class="summary-sig-arg">feature_rank</span>,
<span class="summary-sig-arg">bioentry_id</span>)</span><br />
Load a biopython SeqFeature into the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_seqfeature">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_basic" class="summary-sig-name" onclick="show_private();">_load_seqfeature_basic</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">feature_type</span>,
<span class="summary-sig-arg">feature_rank</span>,
<span class="summary-sig-arg">bioentry_id</span>)</span><br />
Load the first tables of a seqfeature and returns the id.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_seqfeature_basic">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_locations" class="summary-sig-name" onclick="show_private();">_load_seqfeature_locations</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">feature</span>,
<span class="summary-sig-arg">seqfeature_id</span>)</span><br />
Load all of the locations for a SeqFeature into tables.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_seqfeature_locations">source code</a></span>
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<td><span class="summary-sig"><a name="_insert_seqfeature_location"></a><span class="summary-sig-name">_insert_seqfeature_location</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">feature</span>,
<span class="summary-sig-arg">rank</span>,
<span class="summary-sig-arg">seqfeature_id</span>)</span><br />
Add a location of a SeqFeature to the seqfeature_location table.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._insert_seqfeature_location">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_qualifiers" class="summary-sig-name" onclick="show_private();">_load_seqfeature_qualifiers</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">qualifiers</span>,
<span class="summary-sig-arg">seqfeature_id</span>)</span><br />
Insert the (key, value) pair qualifiers relating to a feature.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_seqfeature_qualifiers">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_dbxref" class="summary-sig-name" onclick="show_private();">_load_seqfeature_dbxref</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbxrefs</span>,
<span class="summary-sig-arg">seqfeature_id</span>)</span><br />
Add the database crossreferences of a SeqFeature to the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_seqfeature_dbxref">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_get_dbxref_id" class="summary-sig-name" onclick="show_private();">_get_dbxref_id</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">accession</span>)</span><br />
o db String, the name of the external database containing
the accession number</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_dbxref_id">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_get_seqfeature_dbxref" class="summary-sig-name" onclick="show_private();">_get_seqfeature_dbxref</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">seqfeature_id</span>,
<span class="summary-sig-arg">dbxref_id</span>,
<span class="summary-sig-arg">rank</span>)</span><br />
Check for a pre-existing seqfeature_dbxref entry with the passed
seqfeature_id and dbxref_id.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_seqfeature_dbxref">source code</a></span>
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<td><span class="summary-sig"><a name="_add_seqfeature_dbxref"></a><span class="summary-sig-name">_add_seqfeature_dbxref</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">seqfeature_id</span>,
<span class="summary-sig-arg">dbxref_id</span>,
<span class="summary-sig-arg">rank</span>)</span><br />
Insert a seqfeature_dbxref row and return the seqfeature_id and
dbxref_id</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._add_seqfeature_dbxref">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_load_dbxrefs" class="summary-sig-name" onclick="show_private();">_load_dbxrefs</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>,
<span class="summary-sig-arg">bioentry_id</span>)</span><br />
Load any sequence level cross references into the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_dbxrefs">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_get_bioentry_dbxref" class="summary-sig-name" onclick="show_private();">_get_bioentry_dbxref</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">bioentry_id</span>,
<span class="summary-sig-arg">dbxref_id</span>,
<span class="summary-sig-arg">rank</span>)</span><br />
Check for a pre-existing bioentry_dbxref entry with the passed
seqfeature_id and dbxref_id.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_bioentry_dbxref">source code</a></span>
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<td><span class="summary-sig"><a name="_add_bioentry_dbxref"></a><span class="summary-sig-name">_add_bioentry_dbxref</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">bioentry_id</span>,
<span class="summary-sig-arg">dbxref_id</span>,
<span class="summary-sig-arg">rank</span>)</span><br />
Insert a bioentry_dbxref row and return the seqfeature_id and
dbxref_id</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._add_bioentry_dbxref">source code</a></span>
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<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">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">adaptor</span>,
<span class="sig-arg">dbid</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader.__init__">source code</a></span>
</td>
</tr></table>
<p>Initialize with connection information for the database.</p>
<p>XXX Figure out what I need to load a database and document it.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_get_ontology_id"></a>
<div class="private">
<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_ontology_id</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>,
<span class="sig-arg">definition</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_ontology_id">source code</a></span>
</td>
</tr></table>
<p>Returns the identifier for the named ontology.</p>
<p>This looks through the onotology table for a the given entry name. If
it is not found, a row is added for this ontology (using the definition
if supplied). In either case, the id corresponding to the provided name
is returned, so that you can reference it in another table.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_get_term_id"></a>
<div class="private">
<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_term_id</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>,
<span class="sig-arg">ontology_id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">definition</span>=<span class="sig-default">None</span>,
<span class="sig-arg">identifier</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_term_id">source code</a></span>
</td>
</tr></table>
<p>Get the id that corresponds to a term.</p>
<p>This looks through the term table for a the given term. If it is not
found, a new id corresponding to this term is created. In either case,
the id corresponding to that term is returned, so that you can reference
it in another table.</p>
<p>The ontology_id should be used to disambiguate the term.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_get_taxon_id"></a>
<div class="private">
<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_taxon_id</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="BioSQL.Loader-pysrc.html#DatabaseLoader._get_taxon_id">source code</a></span>
</td>
</tr></table>
<p>Get the taxon id for this record.</p>
<p>record - a SeqRecord object</p>
<p>This searches the taxon/taxon_name tables using the NCBI taxon ID,
scientific name and common name to find the matching taxon table entry's
id.</p>
<p>If the species isn't in the taxon table, and we have at least the NCBI
taxon ID, scientific name or common name, a minimal stub entry is created
in the table.</p>
<p>If this information is not in the record's annotation, then None is
returned.</p>
<p>See also the BioSQL script load_ncbi_taxonomy.pl which will populate
and update the taxon/taxon_name tables with the latest information from
the NCBI.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_bioentry_table"></a>
<div class="private">
<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">_load_bioentry_table</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="BioSQL.Loader-pysrc.html#DatabaseLoader._load_bioentry_table">source code</a></span>
</td>
</tr></table>
<p>Fill the bioentry table with sequence information.</p>
<p>record - SeqRecord object to add to the database.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_bioentry_date"></a>
<div class="private">
<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">_load_bioentry_date</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">record</span>,
<span class="sig-arg">bioentry_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_bioentry_date">source code</a></span>
</td>
</tr></table>
<p>Add the effective date of the entry into the database.</p>
<p>record - a SeqRecord object with an annotated date bioentry_id -
corresponding database identifier</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_biosequence"></a>
<div class="private">
<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">_load_biosequence</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">record</span>,
<span class="sig-arg">bioentry_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_biosequence">source code</a></span>
</td>
</tr></table>
<p>Record a SeqRecord's sequence and alphabet in the database.</p>
<p>record - a SeqRecord object with a seq property bioentry_id -
corresponding database identifier</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_comment"></a>
<div class="private">
<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">_load_comment</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">record</span>,
<span class="sig-arg">bioentry_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_comment">source code</a></span>
</td>
</tr></table>
<p>Record a SeqRecord's annotated comment in the database.</p>
<p>record - a SeqRecord object with an annotated comment bioentry_id -
corresponding database identifier</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_annotations"></a>
<div class="private">
<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">_load_annotations</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">record</span>,
<span class="sig-arg">bioentry_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_annotations">source code</a></span>
</td>
</tr></table>
<p>Record a SeqRecord's misc annotations in the database.</p>
<p>The annotation strings are recorded in the bioentry_qualifier_value
table, except for special cases like the reference, comment and taxonomy
which are handled with their own tables.</p>
<p>record - a SeqRecord object with an annotations dictionary bioentry_id
- corresponding database identifier</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_reference"></a>
<div class="private">
<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">_load_reference</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">reference</span>,
<span class="sig-arg">rank</span>,
<span class="sig-arg">bioentry_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_reference">source code</a></span>
</td>
</tr></table>
<p>Record a SeqRecord's annotated references in the database.</p>
<p>record - a SeqRecord object with annotated references bioentry_id -
corresponding database identifier</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_seqfeature_basic"></a>
<div class="private">
<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">_load_seqfeature_basic</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">feature_type</span>,
<span class="sig-arg">feature_rank</span>,
<span class="sig-arg">bioentry_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_seqfeature_basic">source code</a></span>
</td>
</tr></table>
<p>Load the first tables of a seqfeature and returns the id.</p>
<p>This loads the "key" of the seqfeature (ie. CDS, gene) and
the basic seqfeature table itself.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_seqfeature_locations"></a>
<div class="private">
<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">_load_seqfeature_locations</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">feature</span>,
<span class="sig-arg">seqfeature_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_seqfeature_locations">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Load all of the locations for a SeqFeature into tables.
This adds the locations related to the SeqFeature into the
seqfeature_location table. Fuzzies are not handled right now.
For a simple location, ie (1..2), we have a single table row
with seq_start = 1, seq_end = 2, location_rank = 1.
For split locations, ie (1..2, 3..4, 5..6) we would have three
row tables with:
start = 1, end = 2, rank = 1
start = 3, end = 4, rank = 2
start = 5, end = 6, rank = 3
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_seqfeature_qualifiers"></a>
<div class="private">
<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">_load_seqfeature_qualifiers</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">qualifiers</span>,
<span class="sig-arg">seqfeature_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_seqfeature_qualifiers">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Insert the (key, value) pair qualifiers relating to a feature.
Qualifiers should be a dictionary of the form:
{key : [value1, value2]}
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_seqfeature_dbxref"></a>
<div class="private">
<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">_load_seqfeature_dbxref</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">dbxrefs</span>,
<span class="sig-arg">seqfeature_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_seqfeature_dbxref">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Add the database crossreferences of a SeqFeature to the database.
o dbxrefs List, dbxref data from the source file in the
format <database>:<accession>
o seqfeature_id Int, the identifier for the seqfeature in the
seqfeature table
Insert dbxref qualifier data for a seqfeature into the
seqfeature_dbxref and, if required, dbxref tables.
The dbxref_id qualifier/value sets go into the dbxref table
as dbname, accession, version tuples, with dbxref.dbxref_id
being automatically assigned, and into the seqfeature_dbxref
table as seqfeature_id, dbxref_id, and rank tuples
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_get_dbxref_id"></a>
<div class="private">
<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_dbxref_id</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">db</span>,
<span class="sig-arg">accession</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_dbxref_id">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
o db String, the name of the external database containing
the accession number
o accession String, the accession of the dbxref data
Finds and returns the dbxref_id for the passed data. The method
attempts to find an existing record first, and inserts the data
if there is no record.
</pre>
<dl class="fields">
<dt>Returns: Int</dt>
</dl>
</td></tr></table>
</div>
<a name="_get_seqfeature_dbxref"></a>
<div class="private">
<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_seqfeature_dbxref</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">seqfeature_id</span>,
<span class="sig-arg">dbxref_id</span>,
<span class="sig-arg">rank</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_seqfeature_dbxref">source code</a></span>
</td>
</tr></table>
<p>Check for a pre-existing seqfeature_dbxref entry with the passed
seqfeature_id and dbxref_id. If one does not exist, insert new data</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_load_dbxrefs"></a>
<div class="private">
<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">_load_dbxrefs</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">record</span>,
<span class="sig-arg">bioentry_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._load_dbxrefs">source code</a></span>
</td>
</tr></table>
<p>Load any sequence level cross references into the database.</p>
<p>See table bioentry_dbxref</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_get_bioentry_dbxref"></a>
<div class="private">
<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_bioentry_dbxref</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">bioentry_id</span>,
<span class="sig-arg">dbxref_id</span>,
<span class="sig-arg">rank</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_bioentry_dbxref">source code</a></span>
</td>
</tr></table>
<p>Check for a pre-existing bioentry_dbxref entry with the passed
seqfeature_id and dbxref_id. If one does not exist, insert new data</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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