[Bioperl-l] Problems Bio::DB::Genbank

[Lluis Armengol - Linux]

Some weird things are going on with this module in my computer right now
... It used to work pretty well but right now I get an error like :

> -------------------- EXCEPTION --------------------
> MSG: Attempting to set the sequence to [<HTML] which does not look
healthy
> STACK Bio::PrimarySeq::seq
/usr/lib/perl5/site_perl/5.005/Bio/PrimarySeq.pm:243
> STACK Bio::PrimarySeq::new
/usr/lib/perl5/site_perl/5.005/Bio/PrimarySeq.pm:218
> STACK Bio::Seq::new /usr/lib/perl5/site_perl/5.005/Bio/Seq.pm:133
> STACK Bio::SeqIO::fasta::next_primary_seq
/usr/lib/perl5/site_perl/5.005/Bio/SeqIO/fasta.pm:130
> STACK Bio::SeqIO::fasta::next_seq
/usr/lib/perl5/site_perl/5.005/Bio/SeqIO/fasta.pm:85
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
/usr/lib/perl5/site_perl/5.005/Bio/DB/WebDBSeqI.pm:159
> STACK toplevel /home/armengol/bioperl/retrieveGB.pl:12
> -------------------------------------------

I also paste the script ... I would really appreciate if anyone could
help ...


#!/usr/local/bin/perl
use Bio::DB::GenBank;
use Bio::SeqIO;
$gb = new Bio::DB::GenBank ('-format'=>'Fasta',
-retrievaltype=>'tempfile');
$seqio = new Bio::SeqIO ('-format'=>'Fasta', -file=>">$ARGV[0].tfa");
print "\nRetrieving -> ", $ARGV[0], " from GenBank\n";
$sequence_from_GB = $gb->get_Seq_by_acc([$ARGV[0]]);
$id = $sequence_from_GB->seq();
$seqio->write_seq($sequence_from_GB);
print "$id";
print "\nLa seqüència $ARGV[0] consta de ",$sequence_from_GB->length(),
"bp.\n";


Thanks a lot for your time ...



--
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Lluís Armengol Dulcet
Departament de Genètica Mèdica i Molecular
Institut de Recerca Oncològica
Hospital Duran i Reynals, Ciutat Sanitària de Bellvitge
L'Hospitalet del Llobregat - BARCELONA - CATALUNYA

Tf. 932.607.775
Fx. 932.607.776
llarmengol@iro.es

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