[BioPython] Deprecating Bio.NBRF

Peter biopython at maubp.freeserve.co.uk
Fri Aug 8 11:51:35 UTC 2008


Dear all,

Is anyone using Bio.NBRF for reading NBRF/PIR files?

Good news: I've just added support for reading NBRF/PIR files as
SeqRecord objects to Bio.SeqIO, under the format name "pir" as used in
EMBOSS and BioPerl.  See enhancement Bug 2535,
http://bugzilla.open-bio.org/show_bug.cgi?id=2535

Bad news: I would now like to deprecate the old Bio.NBRF module which
was an NBRF/PIR parser which generated its own record objects (not
SeqRecord objects).  The main reason to drop this module is it relies
on some of Biopython's older parsing infrastructure which depends on
mxTextTools (and doesn't entirely work with mxTextTools 3.0).

So, if anyone if using Bio.NBRF, please get in touch.

Peter



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