Package Bio :: Package config :: Module DBRegistry

Module DBRegistry

Implements Registry to access databases. These objects access databases using a dictionary-like interface, where the key is the ID of the thing to look up, and the value returned is the data associated with the key.

Classes: DBRegistry Accesses databases with a dictionary-like interface. DBObject Base class for Registry objects for databases. DBGroup Groups DBObjects.

CGIDB Accesses CGI databases. EUtilsDB Accesses NCBI using EUtils. BioSQLDB Accesses a BioSQL database. BioCorbaDB Accesses a BioCorba database. IndexedFileDB Accesses a Mindy Indexed file.

Classes

[hide private]

DBRegistry
This implements a dictionary-like interface to databases.

DBObject
This is a base class for dictionary-like interfaces to databases.

DBGroup
Groups DBObjects that return the same kind of data.

TextLikeMixin
Mixin class with useful functionality for retrival of text files.

CGIDB
This class implements DBObject for accessing CGI databases.

EUtilsDB
Implement DBObject for accessing EUtils databases at NCBI.

BioSQLDB
Represent a BioSQL-style database to retrieve SeqRecord objects.

BioCorbaDB
Represent a BioCorba BioSequenceCollection for SeqRecord objects.

IndexedFileDB
Return SeqRecord objects from an indexed file.

Functions

[hide private]

_clean_abbrev(abbrev)

source code

_my_urlencode(params)

source code

Variables

[hide private]

db = db