[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

------------- 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
STACK: Bio::SeqIO::embl::next_seq
STACK: -e:1

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

Jesper Krogh

More information about the Bioperl-l mailing list