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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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Bio::EnsEMBL::IdMapping::Cache - a cache to hold data objects used by the IdMapping application
DESCRIPTION
METHODS
new
Arg [LOGGER]: Bio::EnsEMBL::Utils::Logger $logger - a logger object
Arg [CONF] : Bio::EnsEMBL::Utils::ConfParser $conf - a configuration object
Example : my $cache = Bio::EnsEMBL::IdMapping::Cache->new(
-LOGGER => $logger,
-CONF => $conf,
);
Description : constructor
Return type : Bio::EnsEMBL::IdMapping::Cache object
Exceptions : thrown on wrong or missing arguments
Caller : general
Status : At Risk
: under developmentbuild_cache_by_slice
Arg[1] : String $dbtype - db type (source|target)
Arg[2] : String $slice_name - the name of a slice (format as returned by
Bio::EnsEMBL::Slice->name)
Example : my ($num_genes, $filesize) = $cache->build_cache_by_slice(
'source', 'chromosome:NCBI36:X:1:1000000:-1');
Description : Builds a cache of genes, transcripts, translations and exons
needed by the IdMapping application and serialises the resulting
cache object to a file, one slice at a time.
Return type : list of the number of genes processed and the size of the
serialised cache file
Exceptions : thrown on invalid slice name
Caller : general
Status : At Risk
: under developmentbuild_cache_all
Arg[1] : String $dbtype - db type (source|target)
Example : my ($num_genes, $filesize) = $cache->build_cache_all('source');
Description : Builds a cache of genes, transcripts, translations and exons
needed by the IdMapping application and serialises the
resulting cache object to a file. All genes across the genome
are processed in one go. This method should be used when
build_cache_by_seq_region can't be used due to a large number
of toplevel seq_regions (e.g. 2x genomes).
Return type : list of the number of genes processed and the size of the
serialised cache file
Exceptions : thrown on invalid slice name
Caller : general
Status : At Risk
: under developmentbuild_cache_from_genes
Arg[1] : String $type - cache type
Arg[2] : Listref of Bio::EnsEMBL::Genes $genes - genes to build cache
from
Arg[3] : Boolean $need_project - indicate if we need to project exons to
common coordinate system
Example : $cache->build_cache_from_genes(
'source.chromosome:NCBI36:X:1:100000:1', \@genes);
Description : Builds the cache by fetching transcripts, translations and exons
for a list of genes from the database, and creating lightweight
Bio::EnsEMBL::IdMapping::TinyFeature objects containing only the
data needed by the IdMapping application. These objects are
attached to a name cache in this cache object. Exons only need
to be projected to a commond coordinate system if their native
coordinate system isn't common to source and target assembly
itself.
Return type : int - number of genes after filtering
Exceptions : thrown on wrong or missing arguments
Caller : internal
Status : At Risk
: under developmentfilter_biotypes
Arg[1] : Listref of Bio::EnsEMBL::Genes $genes - the genes to filter
Example : my @filtered = @{ $cache->filter_biotypes(\@genes) };
Description : Filters a list of genes by biotype. Biotypes are
taken from the IdMapping configuration parameter
'biotypes_include' or 'biotypes_exclude'.
If the configuration parameter 'biotypes_exclude' is
defined, then rather than returning the genes whose
biotype is listed in the configuration parameter
'biotypes_include' the method will return the genes
whose biotype is *not* listed in the 'biotypes_exclude'
configuration parameter.
It is an error to define both these configuration
parameters.
The old parameter 'biotypes' is equivalent to
'biotypes_include'.
Return type : Listref of Bio::EnsEMBL::Genes (or empty list)
Exceptions : none
Caller : internal
Status : At Risk
: under developmentadd
Arg[1] : String $name - a cache name (e.g. 'genes_by_id')
Arg[2] : String type - a cache type (e.g. "source.$slice_name")
Arg[3] : String $key - key of this entry (e.g. a gene dbID)
Arg[4] : Bio::EnsEMBL::IdMappping::TinyFeature $val - value to cache
Example : $cache->add('genes_by_id',
'source.chromosome:NCBI36:X:1:1000000:1', '1234', $tiny_gene);
Description : Adds a TinyFeature object to a named cache.
Return type : Bio::EnsEMBL::IdMapping::TinyFeature
Exceptions : thrown on wrong or missing arguments
Caller : internal
Status : At Risk
: under developmentadd_list
Arg[1] : String $name - a cache name (e.g. 'genes_by_id')
Arg[2] : String type - a cache type (e.g. "source.$slice_name")
Arg[3] : String $key - key of this entry (e.g. a gene dbID)
Arg[4] : List of Bio::EnsEMBL::IdMappping::TinyFeature @val - values
to cache
Example : $cache->add_list('transcripts_by_exon_id',
'source.chromosome:NCBI36:X:1:1000000:1', '1234',
$tiny_transcript1, $tiny_transcript2);
Description : Adds a list of TinyFeature objects to a named cache.
Return type : Listref of Bio::EnsEMBL::IdMapping::TinyFeature objects
Exceptions : thrown on wrong or missing arguments
Caller : internal
Status : At Risk
: under development