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]
Represents a BioSQL database continaing namespaces (sub-databases).
A wraper for mysql.connector resolving bytestring representations.
High level wrapper for a database connection and cursor.
A BioSQL Adaptor class with fixes for the MySQL interface.
Represents a namespace (sub-database) within the BioSQL database.
Functions [hide private]
open_database(driver='MySQLdb', **kwargs)
Load an existing BioSQL-style database.
source code
Variables [hide private]
  _interface_specific_adaptors = {'mysql.connector': <class 'Bio...
  _allowed_lookups = {'accession': 'fetch_seqid_by_accession', '...
  __package__ = 'BioSQL'
Function Details [hide private]

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

source code 

Load an 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")
  • 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]


{'mysql.connector': <class 'BioSQL.BioSeqDatabase.MysqlConnectorAdapto\


{'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'}