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Package BioSQL :: Module BioSeqDatabase |
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Connect with a BioSQL database and load Biopython like objects from it.
This provides interfaces for loading biological objects from a relational database, and is compatible with the BioSQL standards.Classes | |
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Adaptor |
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BioSeqDatabase |
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DBServer |
Function Summary | |
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Main interface for loading a existing BioSQL-style database. |
Variable Summary | |
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dict |
_allowed_lookups = {'display_id': 'fetch_seqid_by_displa...
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Function Details |
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open_database(driver='MySQLdb', **kwargs)Main interface for loading a existing BioSQL-style database. This function is the easiest way to retrieve a connection to a database, doing something like:
>>> from BioSeq import BioSeqDatabase
>>> server = BioSeqDatabase.open_database(user = "root", db="minidb")
the various options are: driver -> The name of the database
driver to use for connecting. The driver should implement the python DB
API. By default, the MySQLdb driver is used. user -> the username to
connect to the database with. password, passwd -> the password to
connect with host -> the hostname of the database database or db
-> the name of the database
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Variable Details |
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