[Bioperl-l] Primary seq primary_id?

[Hilmar Lapp]

Sorry I was too fast. Please file it as a bug report.

First, the POD of Bio::Seq::primary_id explicitly states that it is not delegated to the primary_seq. Can anyone remember why this is or why this should stay?

Second, Bio::Seq::new does recognize and honor -primary_id, I overlooked it. Can't be the problem.

Needs to be investigated. Feel welcome to do so ...

	-hilmar

> -----Original Message-----
> From: Hilmar Lapp 
> Sent: Thursday, November 07, 2002 12:04 PM
> To: 'Wiepert, Mathieu'; bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] Primary seq primary_id?
> 
> 
> 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
> > > > _______________________________________________
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> > > > 
> > > 
> > 
>