[Bioperl-l] Error Message

[Heikki Lehvaslaiho]

Ray,

The code is fine, so most probably the problem is with the data file.
Are you sure you have 'seqs.sp' file in your working directory? Does it 
contain at least one valid SWISS-PROT entry? Is the ID line the the very 
first line in the file?

Try replacing seq.sp with the full path to a SWISS-PROT file. This worked 
for me:
'</home/heikki/src/bioperl/core/t/data/SwissProt.dat',


I foud the tutorial from:

http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/

The file 'seqs.sp' is actually saved as 'seqs.sp.text'. Have you changed the
name into one used by the script?


Hope this helps,
			-Heikki


Dibakar Ray wrote:
> I am very new to the world of BioPerl. I am facing few problems. Hope 
> 'gurus' can help me.
> 
>  
> 
> My platform is Linux 6.2
> 
> I have installed bioperl /bioperl-1.0.1/
> I was trying to run the first example shown in the tutorial at 
> http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/1ere_journee.html. 
> 
> 
> The code is given below -
> 
> 
> use Bio::SeqIO;
> 
> my $in  = Bio::SeqIO->newFh ( -file   => '<seqs.sp',
>                               -format => 'swiss' );
> 
> my $out = Bio::SeqIO->newFh ( -file   => '>seqs.fasta',
>                               -format => 'fasta' );
> 
> 
> print $out $_ while <$in>;
> 
> When I try to run it it gives an Error
> 
> -------------------EXCEPTION-------------------------------
> 
> MSG: swissprot stream with no ID. Not swissprot in my book
> 
> STACK Bio::SeqIO::swiss::next_seq 
> /usr/lib/perl5/site_perl/5.005/Bio/SeqIO/Swiss.pm:155
> 
> STACK Bio::SeqIO::READLINE /usr/lib/perl5/site_perl/5.005/Bio/SeqIO.pm:596
> 
> STACK toplevel test3.pl:15
> 
> -------------------------------------------------------------------------------------------------
> 
> So I am struc at the very begining. Looking for some help.
> 
> Regards
> 
> ray
> 


-- 
______ _/      _/_____________________________________________________
       _/      _/                      http://www.ebi.ac.uk/mutations/
      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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