Arbitrary Queries To Ensembl Api In Python (Retrieving Stable Id History)
I would like to be map between Ensembl stable IDs between different releases
I found a small tool to do this in Perl (link) which essentially boils down to connecting to the Ensembl registry:
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db( -host => 'ensembldb.ensembl.org',
-user => 'anonymous' );
my $adaptor = $registry->get_DBAdaptor( $species, 'Core' );
and performing the following query:
SELECT old_version,
old_release,
new_stable_id, new_version,
new_release,
score
FROM stable_id_event
JOIN mapping_session USING (mapping_session_id)
WHERE old_stable_id = ?
ORDER BY old_version ASC, CAST(new_release AS UNSIGNED)
I would like to the same in Python and I looked into pygr/pyensembl which is outdated and pycogent (couldn't figure out how to do this kind of custom query). What's the best way to do the mapping in Python?
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1 answer
Your best bet would be to program against the Ensembl Rest API I would of thought
http://www.ensembl.info/blog/2012/09/27/ensembl-rest-api-ensembl-data-from-any-language/
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