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

[Malcolm Cook]

Lluis,

That error is data dependent.  Look at $ARV[0].tfa file and you will
undoubtedly find that it is not a FASTA file but rather has some HTML in it.

Regards,


Malcolm

> -----Original Message-----
> From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
> Behalf Of Lluis Armengol - Linux
> Sent: Thursday, November 29, 2001 3:21 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Problems Bio::DB::Genbank
>
>
> 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 ...
>
>
>
> --
> ________________________________________________________
>
> 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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