[Biopython-dev] Modules to be removed from Biopython

[Leighton Pritchard]

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.

On 23/09/2008 13:08, "Brad Chapman" <chapmanb at 50mail.com> wrote:

> Hi Peter;
> Thanks for your work cleaning this up.
> 
>> Open questions:
>> * Bio.DBXRef - does anyone known what this is for?
>> * Bio.SGMLExtractor - deprecated in 1.46, ready for removal?
> 
> 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).
> 
> Brad

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
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