Class: Ensembl::Core::DBConnection

Inherits:

DBRegistry::Base

• Object
• ActiveRecord::Base
• DBRegistry::Base
• Ensembl::Core::DBConnection

Defined in:

lib/bio-ensembl/db_connection.rb

Overview

The Ensembl::Core::DBConnection is the actual connection established with the Ensembl server.

Direct Known Subclasses

Analysis, AnalysisDescription, AssemblyException, AssemblyLink, AttribType, CoordSystem, DensityFeature, DensityType, Dna, DnaAlignFeature, Exon, ExonStableId, ExonSupportingFeature, ExonTranscript, ExternalDb, ExternalSynonym, Gene, GeneAttrib, GeneStableId, GoXref, Karyotype, Map, Marker, MarkerFeature, MarkerMapLocation, MarkerSynonym, Meta, MetaCoord, MiscAttrib, MiscFeature, MiscFeatureMiscSet, MiscSet, ObjectXref, OligoArray, OligoFeature, OligoProbe, PredictionExon, PredictionTranscript, ProteinAlignFeature, ProteinFeature, RegulatoryFactor, RegulatoryFeature, RepeatConsensus, RepeatFeature, SeqRegion, SeqRegionAttrib, SimpleFeature, Transcript, TranscriptAttrib, TranscriptStableId, TranscriptSupportingFeature, Translation, TranslationAttrib, TranslationStableId, Xref

Class Method Summary

• .connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {}) ⇒ Object

  The Ensembl::Core::DBConnection#connect method makes the connection to the Ensembl core database for a given species.

• .ensemblgenomes_connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {}) ⇒ Object

Methods inherited from DBRegistry::Base

generic_connect, get_info, get_name_from_db

Class Method Details

.connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {}) ⇒ Object

The Ensembl::Core::DBConnection#connect method makes the connection to the Ensembl core database for a given species. By default, it connects to release 50 for that species. You could use a lower number, but some parts of the API might not work, or worse: give the wrong results.

Examples:

# Connect to release 50 of human
Ensembl::Core::DBConnection.connect('homo_sapiens')

# Connect to release 42 of chicken
Ensembl::Core::DBConnection.connect('gallus_gallus')

Parameters:

• species (String) —

  Species to connect to. Must be in snake_case

• ensembl_release. (Integer) —

  Release to connect to (default = 60)

# File 'lib/bio-ensembl/db_connection.rb', line 158

def self.connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {})
  self.generic_connect('core',species, release,args)
end

.ensemblgenomes_connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {}) ⇒ Object

# File 'lib/bio-ensembl/db_connection.rb', line 162

def self.ensemblgenomes_connect(species, release = Ensembl::ENSEMBL_RELEASE, args={})
  args[:ensembl_genomes] = true
  self.generic_connect('core',species,release,args)
end