Class: Ensembl::Core::AssemblyException

Inherits:

DBConnection

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

Includes:

Sliceable

Defined in:

lib/bio-ensembl/core/activerecord.rb

Overview

The AssemblyException class describes the exceptions in to AssemblyLink. Most notably, this concerns the allosomes. In human, for example, only the part of the Y chromosome that is different from X is covered in the assembly table. Therefore, the sequence of the tip and end of the Y chromosome are not stored in the database, but fetched from the X chromosome. The assembly_exception table contain the information on which bits are the same.

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.

This class should normally not be used directly by the user.

Method Summary

Methods included from Sliceable

#length, #project, #seq, #slice, #start, #stop, #strand, #transform

Methods inherited from DBConnection

connect, ensemblgenomes_connect

Methods inherited from DBRegistry::Base

generic_connect, get_info, get_name_from_db