Package Bio :: Package config :: Module DBRegistry :: Class IndexedFileDB
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Class IndexedFileDB

RegisterableObject --+    
                     |    
              DBObject --+
                         |
                        IndexedFileDB


Return SeqRecord objects from an indexed file.

This module deals with both flat file and BerkeleyDB indexes. These indexed files can be created by any of the compliant indexing implementations from Biopython, BioPerl, BioJava, etc...
Method Summary
  __init__(self, name, dbname, doc)
Intialize with information about loading the database.
  _convert_to(self, handle, to_io)
  _get(self, key)
Do the database retrieval of the sequence, returning a handle.
  _get_check_names(self, given_name, db)
Get a list of all namespaces to search for the file under.
  _load_database(self, name)
Get a connection with the given database.
    Inherited from DBObject
  __getitem__(self, key)
  get(self, key, default)
S.get(key[, default]) -> data
  get_as(self, key, to_io, default)
S.get_as(key[, to_io][, default]) -> object
  set(self, key, data)
  _make_pickleable(self, data)
S._make_pickleable(key, data) -> pickleable_obj
  _set(self, key, data)
S._set(key, data)
  _unmake_pickleable(self, pickleable_obj)
S._unmake_pickleable(key, pickleable_obj) -> data

Method Details

__init__(self, name, dbname, doc='')
(Constructor)

Intialize with information about loading the database.

dbname is the name of the database to open. This will likely be a filesystem path to a database directory.
Overrides:
Bio.config.DBRegistry.DBObject.__init__

_get(self, key)

Do the database retrieval of the sequence, returning a handle.
Overrides:
Bio.config.DBRegistry.DBObject._get

_get_check_names(self, given_name, db)

Get a list of all namespaces to search for the file under.

If given_name is a valid key, then it is returned as the only thing to check. Otherwise, we go forward and check all possible namespaces.

_load_database(self, name)

Get a connection with the given database.

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