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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>Object used to load SeqRecord objects into a BioSQL database.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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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 class="summary-sig-arg">fetch_NCBI_taxonomy</span>=<span class="summary-sig-default">False</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>
<td align="right" valign="top">
<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 (PRIVATE).</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 (PRIVATE).</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>
<td align="right" valign="top">
<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 (PRIVATE).</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#_fix_name_class" class="summary-sig-name" onclick="show_private();">_fix_name_class</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">entrez_name</span>)</span><br />
Map Entrez name terms to those used in taxdump (PRIVATE).</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._fix_name_class">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_get_taxon_id_from_ncbi_taxon_id" class="summary-sig-name" onclick="show_private();">_get_taxon_id_from_ncbi_taxon_id</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">ncbi_taxon_id</span>,
<span class="summary-sig-arg">scientific_name</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">common_name</span>=<span class="summary-sig-default">None</span>)</span><br />
Get the taxon id for this record from the NCBI taxon ID (PRIVATE).</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_taxon_id_from_ncbi_taxon_id">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.Loader.DatabaseLoader-class.html#_get_taxon_id_from_ncbi_lineage" class="summary-sig-name" onclick="show_private();">_get_taxon_id_from_ncbi_lineage</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">taxonomic_lineage</span>)</span><br />
This is recursive! (PRIVATE).</td>
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<span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_taxon_id_from_ncbi_lineage">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 (PRIVATE).</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 (PRIVATE).</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 (PRIVATE).</td>
<td align="right" valign="top">
<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 (PRIVATE).</td>
<td align="right" valign="top">
<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 (PRIVATE).</td>
<td align="right" valign="top">
<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 (PRIVATE).</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 (PRIVATE).</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 (PRIVATE).</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 href="BioSQL.Loader.DatabaseLoader-class.html#_insert_seqfeature_location" class="summary-sig-name" onclick="show_private();">_insert_seqfeature_location</a>(<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
(PRIVATE).</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 (PRIVATE).</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 database crossreferences of a SeqFeature to the database (PRIVATE).</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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<tr>
<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 (PRIVATE).</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>
</td>
</tr>
<tr class="private">
<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.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>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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 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>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></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">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">adaptor</span>,
<span class="sig-arg">dbid</span>,
<span class="sig-arg">fetch_NCBI_taxonomy</span>=<span class="sig-default">False</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>
<pre class="literalblock">
Initialize with connection information for the database.
Creating a DatabaseLoader object is normally handled via the
BioSeqDatabase DBServer object, for example:
from BioSQL import BioSeqDatabase
server = BioSeqDatabase.open_database(driver="MySQLdb", user="gbrowse",
passwd = "biosql", host = "localhost", db="test_biosql")
try:
db = server["test"]
except KeyError:
db = server.new_database("test", description="For testing GBrowse")
</pre>
<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 (PRIVATE).</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 (PRIVATE).</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 (PRIVATE).</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, at least a minimal stub entry
is created in the table.</p>
<p>Returns the taxon id (database key for the taxon table, not an NCBI
taxon ID), or None if the taxonomy information is missing.</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="_fix_name_class"></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">_fix_name_class</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">entrez_name</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._fix_name_class">source code</a></span>
</td>
</tr></table>
<p>Map Entrez name terms to those used in taxdump (PRIVATE).</p>
<p>We need to make this conversion to match the taxon_name.name_class
values used by the BioSQL load_ncbi_taxonomy.pl script.</p>
<p>e.g. "ScientificName" -> "scientific name",
"EquivalentName" -> "equivalent name",
"Synonym" -> "synonym",</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_get_taxon_id_from_ncbi_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_from_ncbi_taxon_id</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">ncbi_taxon_id</span>,
<span class="sig-arg">scientific_name</span>=<span class="sig-default">None</span>,
<span class="sig-arg">common_name</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_taxon_id_from_ncbi_taxon_id">source code</a></span>
</td>
</tr></table>
<p>Get the taxon id for this record from the NCBI taxon ID (PRIVATE).</p>
<p>ncbi_taxon_id - string containing an NCBI taxon id scientific_name -
string, used if a stub entry is recorded common_name - string, used if a
stub entry is recorded</p>
<p>This searches the taxon table using ONLY the NCBI taxon ID to find the
matching taxon table entry's ID (database key).</p>
<p>If the species isn't in the taxon table, and the fetch_NCBI_taxonomy
flag is true, Biopython will attempt to go online using Bio.Entrez to
fetch the official NCBI lineage, recursing up the tree until an existing
entry is found in the database or the full lineage has been fetched.</p>
<p>Otherwise the NCBI taxon ID, scientific name and common name are
recorded as a minimal stub entry in the taxon and taxon_name tables. Any
partial information about the lineage from the SeqRecord is NOT recorded.
This should mean that (re)running the BioSQL script load_ncbi_taxonomy.pl
can fill in the taxonomy lineage.</p>
<p>Returns the taxon id (database key for the taxon table, not an NCBI
taxon ID).</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_get_taxon_id_from_ncbi_lineage"></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_from_ncbi_lineage</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">taxonomic_lineage</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.Loader-pysrc.html#DatabaseLoader._get_taxon_id_from_ncbi_lineage">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
This is recursive! (PRIVATE).
taxonomic_lineage - list of taxonomy dictionaries from Bio.Entrez
First dictionary in list is the taxonomy root, highest would be the species.
Each dictionary includes:
- TaxID (string, NCBI taxon id)
- Rank (string, e.g. "species", "genus", ..., "phylum", ...)
- ScientificName (string)
(and that is all at the time of writing)
This method will record all the lineage given, returning the the taxon id
(database key, not NCBI taxon id) of the final entry (the species).
</pre>
<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 (PRIVATE).</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
(PRIVATE).</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 (PRIVATE).</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 (PRIVATE).</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
(PRIVATE).</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
(PRIVATE).</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 (PRIVATE).
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="_insert_seqfeature_location"></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">_insert_seqfeature_location</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">feature</span>,
<span class="sig-arg">rank</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._insert_seqfeature_location">source code</a></span>
</td>
</tr></table>
<p>Add a location of a SeqFeature to the seqfeature_location table
(PRIVATE).</p>
<p>TODO - Add location_operators to location_qualifier_value.</p>
<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 (PRIVATE).
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 database crossreferences of a SeqFeature to the database (PRIVATE).
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
(PRIVATE).</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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