BioSQL.Loader module¶
Load biopython objects into a BioSQL database for persistent storage.
This code makes it possible to store biopython objects in a relational database and then retrieve them back. You shouldn’t use any of the classes in this module directly. Rather, call the load() method on a database object.
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class
BioSQL.Loader.
DatabaseLoader
(adaptor, dbid, fetch_NCBI_taxonomy=False)¶ Bases:
object
Object used to load SeqRecord objects into a BioSQL database.
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__init__
(self, adaptor, dbid, fetch_NCBI_taxonomy=False)¶ Initialize with connection information for the database.
Creating a DatabaseLoader object is normally handled via the BioSeqDatabase DBServer object, for example:
from BioSQL import BioSeqDatabase server = BioSeqDatabase.open_database(driver="MySQLdb", user="gbrowse", passwd="biosql", host="localhost", db="test_biosql") try: db = server["test"] except KeyError: db = server.new_database("test", description="For testing GBrowse")
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load_seqrecord
(self, record)¶ Load a Biopython SeqRecord into the database.
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class
BioSQL.Loader.
DatabaseRemover
(adaptor, dbid)¶ Bases:
object
Complement the Loader functionality by fully removing a database.
This probably isn’t really useful for normal purposes, since you can just do a:
DROP DATABASE db_name
and then recreate the database. But, it’s really useful for testing purposes.
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__init__
(self, adaptor, dbid)¶ Initialize with a database id and adaptor connection.
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remove
(self)¶ Remove everything related to the given database id.
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