[Bioperl-l] Primary seq primary_id?

[Hilmar Lapp]

By calling $input->primary_id() :) Interestingly I just realized the fasta parser is among the few that set this property. It also appears to be recognized by PrimarySeq::new ... weird. File it as a bug report, I or others need to see whether we can reproduce this.

You rarely want primary_id() BTW. A primary_id would be the GenBank GI number as an example. Usually what you're after for fasta-returned seqs is display_id.

Ahem. I just see this _IS_ a bug. The problem is Bio::Seq implements primary_id itself, which it shouldn't do (it should delegate to the primary_seq object). Bio::Seq::new doesn't honor -primary_id (which is OK if it delegated).

I'll fix this in a second.

	-hilmar

> -----Original Message-----
> From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu]
> Sent: Thursday, November 07, 2002 11:49 AM
> To: Hilmar Lapp; bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] Primary seq primary_id?
> 
> 
> 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
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > > 
> > 
>