[Bioperl-l] Bio::SeqIO::embl probelms reading swissprot

Murad Nayal murad@godel.bioc.columbia.edu
Mon, 11 Dec 2000 20:27:38 +0100

Hello All,

It seems that Bio::SeqIO::embl is having some problems reading
swissprot.dat file. (bioperl 0.6.2 and swissprot 38). for example it
does not match alternative formats for the DR record which leads it to
not instantiate the corresponding DBLink object and occasionally crash.
I have started fixing some of this stuff but I thought I'd check with
the list first.

-is Bio::SeqIO::embl 'supposed' to be able to read swissprot? or is
there another implementation of SeqIO to do that (which I couldn't find
in the 0.6.2 distribution).

-Have these bugs been reported/fixed already in the 0.7 distribution.

-when will 0.7 be available? (is read access to CVS available now to

PS: I should mention that I am encountering these problems when
accessing the .dat file via an Index!


Murad Nayal M.D. Ph.D.
Department of Biochemistry and Molecular Biophysics
College of Physicians and Surgeons of Columbia University
630 West 168th Street. New York, NY 10032
Tel: 212-305-6884	Fax: 212-305-6926