[ensembl-dev] VEP cache and local database

[Michael Yourshaw]

I normally use a local copy of the mySQL database to process large datasets. Some of my plugins make calls to the Ensembl database via the Perl API.

VEP runs normally without the cache.

I want to take advantage of some of the options available only through the cache, such as maf_esp, and possibly improve throughput, but still get everything not in the cache from the local database.

I have downloaded and installed the homo_sapiens_73 cache, and use these parameters:
	cache=1
	dir_cache=/scratch1/tmp/myourshaw/ensembl/.vep/
-—offline is not on

There are two problems when I turn on the cache.

First, some of my plugins get an error in Bio::EnsEMBL::DBSQL::GeneAdaptor in the fetch_nearest_Gene_by_Feature sub at the line
	my $seq_region_id = $feat->slice->adaptor->get_seq_region_id($feat->slice);

The error is
	Can't call method "get_seq_region_id" on an undefined value at /share/apps/myourshaw/ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm line 1978.

Specifically, $feat->slice->adapter is undef

The call in my code that triggers this is:
sub run {
    my ($self, $bvfoa, $line_hash) = @_;
    if($bvfoa->isa('Bio::EnsEMBL::Variation::RegulatoryFeatureVariationAllele')){
        my $feature = $bvfoa->regulatory_feature;
	# At this point, $feature->slice->adapter is undef and the next line fails
        my $nearest_genes = $config->{ga}->fetch_nearest_Gene_by_Feature($feature);
        my $gene = @{$nearest_genes}[0];
    }

Second, I get the following warning when VEP initializes. Is this related to the first problem? Should I be concerned?
	MSG: You are using the API without caching most recent features. Performance might be affected.
	FILE: EnsEMBL/DBSQL/BaseFeatureAdaptor.pm LINE: 76
	CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 1043
	Date (localtime)    = Thu Nov 14 11:52:27 2013
	Ensembl API version = 73


ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

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