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

Sendu Bala bix at sendu.me.uk
Thu Mar 29 05:30:07 EDT 2007

Ambrose wrote:
> 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.

Not sure what you mean by that. The error message is generated by 
BioPerl, so of course you were still using BioPerl.

>    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.

Taxon.pm is new (not 'changed'), and the error is generated by 
Bio::DB::Taxonomy::list, also new.

> Here you are with the error message
> Q0QB51_9DIPT
> Q0QB52_9DIPT
> Q0QB62_9DIPT
> Q0QB63_9DIPT
> ------------- EXCEPTION  -------------
> MSG: The lineage 'Eukaryota, Metazoa, Mollusca, Bivalvia, 
> Heteroconchia,
> Veneroida, Veneroidea, Veneridae, Venerupis, Ruditapes, Venerupis' had 
> two
> non-consecutive nodes with the same name. Can't cope!
> STACK Bio::DB::Taxonomy::list::add_lineage
> /usr/local/ActivePerl/site/lib/Bio/DB/Taxonomy/list.pm:157

Please send me the actual record that causes the exception and I'll see 
what I can do about fixing the problem.

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