[Biopython-dev] Modules to be removed from Biopython

Peter biopython at maubp.freeserve.co.uk
Thu Oct 9 15:31:04 UTC 2008

Leighton Pritchard wrote:
> Hi all,
> It looks like Bio.DBXRef provides a dictionary of dictionaries that
> associate database identifiers from a number of file formats with the
> appropriate databases.  This sort of thing might be useful to keep around
> (i.e. not to have to rebuild from scratch) if there is an intention to
> populate the dbxref table with consistent Dbnames for divergent identifiers.
> However, Peter appears to have noted in the code for Loader.py that this
> behaviour would be inconsistent with the other Bio* projects, and mentions
> bug 2405 in that context.
> L.

As things stand, we don't used this kind of mapping in BioSQL, so I
see no reason not to deprecate Bio.DBXRefs now.  Of course, I can be
talked out of this if anyone has a good use case example.

Brad wrote:
>> DBXref is associated with all the Martel parsing, so it can be
>> removed/deprecated as well. It was used in building SeqRecords from
>> Martel descriptions (Bio.builders.SeqRecord.sequence).

I've just marked Bio.DBXRef as deprecated for 1.49.  Returning to an
earlier point on this thread, I have also removed Bio.SGMLExtractor
(which was deprecated in 1.46).  I think that wraps up the
Martel/Mindy deprecations for now - in a few releases time we'll have
the much simpler task of removing these modules.


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