Package BioSQL :: Module BioSeqDatabase
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Module BioSeqDatabase

source code

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 [hide private]
  DBServer
  Adaptor
  BioSeqDatabase
Functions [hide private]
 
open_database(driver='MySQLdb', **kwargs)
Main interface for loading a existing BioSQL-style database.
source code
Variables [hide private]
  _allowed_lookups = {'accession': 'fetch_seqid_by_accession', '...
  __package__ = 'BioSQL'
Function Details [hide private]

open_database(driver='MySQLdb', **kwargs)

source code 

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


Variables Details [hide private]

_allowed_lookups

Value:
{'accession': 'fetch_seqid_by_accession',
 'display_id': 'fetch_seqid_by_display_id',
 'gi': 'fetch_seqid_by_identifier',
 'name': 'fetch_seqid_by_display_id',
 'primary_id': 'fetch_seqid_by_identifier',
 'version': 'fetch_seqid_by_version'}