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Class: IndexedFile Bio/sources/__init__.py

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...

Base Classes   
Source
Methods   
__init__
_get_check_names
_load_database
_post_process
_rawget
  __init__ 
__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.

  _get_check_names 
_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 
_load_database ( self,  name )

Get a connection with the given database.

  _post_process 
_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.

  _rawget 
_rawget ( self,  params )

Do the database retrieval of the sequence, returning a handle.


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