Package Bio :: Package config :: Module DBRegistry :: Class BioSQLDB
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Class BioSQLDB

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Registry.RegisterableObject --+    
                              |    
                       DBObject --+
                                  |
                                 BioSQLDB

Represent a BioSQL-style database to retrieve SeqRecord objects.

This returns a SeqRecord-like object from _get() instead of a handle (since BioSQL is not going to give you a handle).

Instance Methods [hide private]
 
__init__(self, name, doc='', db_host='localhost', db_port='', db_user='root', db_passwd='', sql_db='', namespace_db='', db_type='mysql')
Intialize with information for connecting to the BioSQL db.
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_get_db_module(self, db_type)
Retrieve the appropriate module to use for connecting to a database
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data
_get(self, key) source code
another data type
_convert_to(self, data, to_io) source code
pickleable_obj
_make_pickleable(self, item) source code
data
_unmake_pickleable(self, item) source code

Inherited from DBObject: __getitem__, get, get_as, set

Inherited from DBObject (private): _set

Method Details [hide private]

__init__(self, name, doc='', db_host='localhost', db_port='', db_user='root', db_passwd='', sql_db='', namespace_db='', db_type='mysql')
(Constructor)

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Intialize with information for connecting to the BioSQL db.

Overrides: Registry.RegisterableObject.__init__

_get_db_module(self, db_type)

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Retrieve the appropriate module to use for connecting to a database

This parses a description of the database and tries to determine which module is appropriate for that database type.

_get(self, key)

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Returns: data
Overrides: DBObject._get
(inherited documentation)

_convert_to(self, data, to_io)

source code 
Returns: another data type
Overrides: DBObject._convert_to
(inherited documentation)

_make_pickleable(self, item)

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Returns: pickleable_obj
Overrides: DBObject._make_pickleable
(inherited documentation)

_unmake_pickleable(self, item)

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Returns: data
Overrides: DBObject._unmake_pickleable
(inherited documentation)