[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
ambrose


Here you are with the error message

Q0QAY1_9DIPT
Q0QAY7_9DIPT
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
STACK Bio::DB::Taxonomy::list::new
/usr/local/ActivePerl/site/lib/Bio/DB/Taxonomy/list.pm:94
STACK Bio::DB::Taxonomy::new
/usr/local/ActivePerl/site/lib/Bio/DB/Taxonomy.pm:103
STACK Bio::Species::classification
/usr/local/ActivePerl/site/lib/Bio/Species.pm:179
STACK Bio::SeqIO::swiss::_read_swissprot_Species
/usr/local/ActivePerl/site/lib/Bio/SeqIO/swiss.pm:1067
STACK Bio::SeqIO::swiss::next_seq
/usr/local/ActivePerl/site/lib/Bio/SeqIO/swiss.pm:247
STACK toplevel upparser.pl:178

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