[Bioperl-l] Error message

CHANDAN SINGH chandan.kr.singh at gmail.com
Tue Jun 20 10:46:01 EDT 2006


Hi
It seems the 'swall' servertype on EBI no longer exists. May be this  has
already been reported  and debugged. I hope somebody throws light on it.

As for George, if u r in hurry u can use Bio::DB::SwissProt module directly.
Here is a typical code to do this

use strict ;
use warnings ;
use Bio::DB::SwissProt ;
use Bio::Perl ;
my $seq_obj = new Bio::DB::SwissProt('-servertype' => 'expasy' ,
'-hostlocation' => 'us') ;
my $seq = $seq_obj->get_Seq_by_id('ROA1_HUMAN') ;
write_sequence("> roa.sp" , 'fasta' , $seq) ;


See the module for any help .

cheers
Chandan


On 6/20/06, George Tzotzos <G.Tzotzos at unido.org> wrote:
>
> I'm a BioPerl novice. I used CPAN to install BioPerl and run the
> following script to test the installation:
>
> use Bio::Perl;
> use strict;
> use warnings;
>
> my $seq_object = get_sequence('swissprot', "P09651");
>
> write_sequence(">roa1.fasta", 'fasta', $seq_object);
>
> I used as argument both "ROA1_HUMAN" and "P09651". In both cases I
> get the message below.
>
> Any help on the nature of the problem and how to overcome it would be
> greatly appreciated.
>
> Thanks
>
> George
>
>
> ------------- EXCEPTION  -------------
> MSG: swissprot stream with no ID. Not swissprot in my book
> STACK Bio::SeqIO::swiss::next_seq /Library/Perl/5.8.6/Bio/SeqIO/
> swiss.pm:179
> STACK Bio::DB::WebDBSeqI::get_Seq_by_id /Library/Perl/5.8.6/Bio/DB/
> WebDBSeqI.pm:153
> STACK Bio::Perl::get_sequence /Library/Perl/5.8.6/Bio/Perl.pm:513
> STACK toplevel tut2.pl:5
>
>
>
>
>
> George T. Tzotzos Ph.D
>
> Wagramerstrasse 5
> A-1400 Vienna
> Austria
>
> Email: g.tzotzos at unido.org
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


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