class Ensembl::Variation::DBConnection

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

Public Class Methods

connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {}) click to toggle source

The Ensembl::Variation::DBConnection#connect method makes the connection to the Ensembl variation 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.

@example

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

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

@param [String] species Species to connect to. Must be in snake_case @param [Integer] ensembl_release. Release to connect to (default = 60)

# File lib/bio-ensembl/db_connection.rb, line 192
def self.connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {})
  self.generic_connect('variation',species, release, args)
end
ensemblgenomes_connect(species, release = Ensembl::ENSEMBL_RELEASE, args={}) click to toggle source
# File lib/bio-ensembl/db_connection.rb, line 196
def self.ensemblgenomes_connect(species, release = Ensembl::ENSEMBL_RELEASE, args={})
  args[:ensembl_genomes] = true
  self.generic_connect('variation',species,release,args)
end