[Bioperl-l] Possible bug in Bio::SeqIO::embl.pm

Jesper Krogh jesper at krogh.cc
Tue Jun 26 03:05:32 EDT 2007


Hi List.

Trying to parse the embl database, the embl-parser fails on: AB019196
http://www.ebi.ac.uk/cgi-bin/expasyfetch?AB019196


------------- 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/Root.pm:359
STACK: Bio::SeqIO::embl::_read_EMBL_Species
/usr/share/perl/5.8/Bio/SeqIO/embl.pm:1091
STACK: Bio::SeqIO::embl::next_seq
/usr/share/perl/5.8/Bio/SeqIO/embl.pm:322
STACK: -e:1
-----------------------------------------------------------


It seems to be dissatisfied with this:
OS   Acetobacter aceti
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales;
OC   Acetobacteraceae; Acetobacter; Acetobacter subgen. Acetobacter.

Thanks.
-- 
Jesper Krogh




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