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Package Bio :: Package config :: Module DBRegistry :: Class IndexedFileDB |
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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 | |
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Intialize with information about loading the database. | |
_convert_to(self,
handle,
to_io)
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Do the database retrieval of the sequence, returning a handle. | |
Get a list of all namespaces to search for the file under. | |
Get a connection with the given database. | |
Inherited from DBObject | |
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S.get(key[, default]) -> data | |
S.get_as(key[, to_io][, default]) -> object | |
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S._make_pickleable(key, data) -> pickleable_obj | |
S._set(key, data) | |
S._unmake_pickleable(key, pickleable_obj) -> data |
Method Details |
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__init__(self,
name,
dbname,
doc='')
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_get(self, key)Do the database retrieval of the sequence, returning a handle.
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_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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