[Bioperl-l] Possible bug in Bio::SeqIO::embl.pm
cjfields at uiuc.edu
Tue Jun 26 10:02:29 EDT 2007
Ill try getting to that ASAP (as well as a few bugs). The problem is
we have to patch this in 2-3 places (SeqIO::swiss, SeqIO::embl) due
to repeated code issues, something I'm trying to rectify with a new
set of parsers. Just haven't had the time to work on them lately
On Jun 26, 2007, at 8:45 AM, Roy Chaudhuri wrote:
> Sorry, replied to this but forgot to cc the list.
> It looks like a related problem to bug 2288 that I filed about
> Bio::SeqIO::swiss - the period after subgen. is what causes the
> problems since it is interpreted as a seperator between nodes. I
> put a patch in for Bio::SeqIO::swiss that works for me, but I guess
> it might have side effects.
> Dr. Roy Chaudhuri
> Department of Veterinary Medicine
> University of Cambridge, U.K.
> Chris Fields wrote:
>> I can verify this using bioperl-live. Can you file this as a bug?
>> On Jun 26, 2007, at 2:05 AM, Jesper Krogh wrote:
>>> Hi List.
>>> Trying to parse the embl database, the embl-parser fails on:
>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: AB019196 seems to have an invalid species classification.
>>> STACK: Error::throw
>>> STACK: Bio::Root::Root::throw /usr/share/perl/5.8/Bio/Root/
>>> STACK: Bio::SeqIO::embl::_read_EMBL_Species
>>> STACK: Bio::SeqIO::embl::next_seq
>>> STACK: -e:1
>>> It seems to be dissatisfied with this:
>>> OS Acetobacter aceti
>>> OC Bacteria; Proteobacteria; Alphaproteobacteria;
>>> OC Acetobacteraceae; Acetobacter; Acetobacter subgen. Acetobacter.
>>> Jesper Krogh
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
More information about the Bioperl-l