Class: Ensembl::Core::AssemblyLink

Inherits:

DBConnection

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

show all

Defined in:: lib/bio-ensembl/core/activerecord.rb

Overview

The AssemblyLink class describes the relationships between different seq_regions. For example, a chromosome might consist of a number of scaffolds, each of which in turn consists of a number of contigs. The AssemblyLink class This class is an interface to the assembly table of the Ensembl mysql database.

This class uses ActiveRecord to access data in the Ensembl database. See the general documentation of the Ensembl module for more information on what this means and what methods are available.

Examples:

chr4 = SeqRegion.find_by_name('4')
puts chr4.coord_system.name     #--> 'chromosome'
chr4.genes.each do |gene|
  puts gene.biotype
end

Method Summary

Methods inherited from DBConnection

connect, ensemblgenomes_connect

Methods inherited from DBRegistry::Base

generic_connect, get_info, get_name_from_db