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...
Methods
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__init__
_get_check_names
_load_database
_post_process
_rawget
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__init__
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__init__ (
self,
name,
doc="",
dbname="",
)
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.
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_get_check_names
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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.
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_load_database
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_load_database ( self, name )
Get a connection with the given database.
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_post_process
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_post_process ( self, handle )
Try to parse the results of a query into a SeqRecord.
This uses Martel auto-detection to try to determine the
format of a file. If the format cannot be determined, the
handle itself is returned.
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_rawget
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_rawget ( self, params )
Do the database retrieval of the sequence, returning a handle.
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