Represent a BioSQL-style database to retrieve SeqRecord objects.
XXX This returns a SeqRecord-like object from get() instead of
a handle (since BioSQL is not going to give you a handle). This
should be standardized.
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Methods
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__init__
_get_db_module
_rawget
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__init__
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__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
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_get_db_module ( self, db_type )
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.
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Exceptions
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ValueError( "Postgres not supported yet. Sorry." )
ValueError( "Unknown database type: %s" % db_type )
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_rawget
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_rawget ( self, params )
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Exceptions
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KeyError( "Could not get item with id: %s" % find_id )
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