[Biopython-dev] [Bug 2361] Test Suite Failures from Martel/Sax with egenix mxTextTools 3.0

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http://bugzilla.open-bio.org/show_bug.cgi?id=2361





------- Comment #20 from biopython-bugzilla at maubp.freeserve.co.uk  2007-09-13 07:27 EST -------
Note that there are other index_file functions in Bio.GenBank and Bio.SwissProt
The Bio.Fasta index_file/Dictionary is also used in several other modules
including the SCOP Astral class (indexing a Fasta file to serve as a database).
 So depreciating it isn't quite as trivial as it could be!

For anyone unfamiliar with the details, note that while Bio.SeqIO.to_dict()
achieves a similar aim, it is done in memory.  The Mindy based
index_file/Dictionary classes parse the file once to create a lookup table on
disk allowing random access to any record in the file.  This functionality was
probably more important historically (lower memory on desktop computers), and
seems to be a mid point between the simple in memory dictionary and a full
blown SQL database.


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