[Bioperl-l] Primary seq primary_id?

[Wiepert, Mathieu]

Hi,

So I am confused then.  The primary_id is set, that is what I wanted, the object looks like this.  Should the primary_id slot not be filled in this case?  The primary id was set in the fast.pm module, in the next_seq sub.  I don't have an accession number.

This is what the object is looking like to me...
0  Bio::Seq=HASH(0x853cfe0)
   'primary_seq' => Bio::PrimarySeq=HASH(0x853cfbc)
      'alphabet' => 'protein'
      'desc' => 'fragment'
      'display_id' => 'CYS1_DICDI'
      'primary_id' => 'CYS1_DICDI'
      'seq' => 'SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE'

How am I supposed to get CYS1_DICDI from the primary_id field?

-Mat

> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp@gnf.org]
> Sent: Thursday, November 07, 2002 1:42 PM
> To: Wiepert, Mathieu; bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] Primary seq primary_id?
> 
> 
> You do get a string. It's just the memory location of the 
> object to fulfill the requirement to return something which 
> is unique in the application. If you don't like that string, 
> set e.g. $input->primary_id($input->accession_number).
> 
> 	-hilmar
> 
> > -----Original Message-----
> > From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu]
> > Sent: Thursday, November 07, 2002 10:42 AM
> > To: 'bioperl-l@bioperl.org'
> > Subject: [Bioperl-l] Primary seq primary_id?
> > 
> > 
> > Hi,
> > 
> > I am pretty sure that something is messed up for me.  When I 
> > call Bio::Seq to get the primary_id of a sequence, I no 
> > longer get a string...
> > 
> > my $seq = Bio::SeqIO->new(-file=>'amino.fa' , '-format' => 
> 'fasta' );
> > my $input = $seq->next_seq();
> > my $primary_id = $input->primary_id;
> > print $primary_id;
> > 
> > gives me
> > 
> > Bio::Seq=HASH(0x82d88d4)
> > 
> > Is there something really silly that I missed somewhere?  I 
> > used to get strings...
> > 
> > -Mat
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> > 
>