Package BioSQL :: Module BioSeqDatabase

Module BioSeqDatabase

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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DBServer
Represents a BioSQL database continaing namespaces (sub-databases).

Adaptor

BioSeqDatabase
Represents a namespace (sub-database) within the BioSQL database.

Functions

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open_database(driver='MySQLdb', **kwargs)
Main interface for loading a existing BioSQL-style database. source code

Variables

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_POSTGRES_RULES_PRESENT = False

_allowed_lookups = {'accession': 'fetch_seqid_by_accession', '...

Function Details

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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

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_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'}

Module BioSeqDatabase

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

_allowed_lookups

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