[Bioperl-l] problem while parsing UniProt(ltaxon.pm)

Ambrose aharry2001 at yahoo.com
Thu Mar 29 04:21:12 EDT 2007

Dear all,
        I am parsing the information in UniProt using bioperl
The parser runs successfull for thousand of records and suddenly I get an error 
message concerning the lineage.The error message suggested that the error
comes up when bioperl tries to parse OC lines(taxonomy).
I decided to parse this out using perl and not bioperl but
I still get the same error message.
   I really wish to know whether the problem is with a 
change in the taxon.pm or has this been problem been reported
by other users.I am waiting ansciously to read from you.
best regards

Here you are with the error message


------------- EXCEPTION  -------------
MSG: The lineage 'Eukaryota, Metazoa, Mollusca, Bivalvia, 
Veneroida, Veneroidea, Veneridae, Venerupis, Ruditapes, Venerupis' had 
non-consecutive nodes with the same name. Can't cope!
STACK Bio::DB::Taxonomy::list::add_lineage
STACK Bio::DB::Taxonomy::list::new
STACK Bio::DB::Taxonomy::new
STACK Bio::Species::classification
STACK Bio::SeqIO::swiss::_read_swissprot_Species
STACK Bio::SeqIO::swiss::next_seq
STACK toplevel upparser.pl:178


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