[Bioperl-l] Tag handling on SeqFeature::Generic

[Jason Stajich]

On Wed, 28 Aug 2002, Marco Aurelio Valtas Cunha wrote:

> Hi Jason,
>
> I'm not intended to violate any API. The reason for such approach is
> generate GFF file for Lincoln's gbrowse (www.gmod.org) mapping tool.
> Gbrowse need something like (GFF):
>
> Contig1 blastn similarity 10 40 . +  . Target "Sequence:Contig3" 1 500
>
> Where Target "Sequence:$mysequence" is the tag that changes for each
> mapped sequence in my case. What happened is that after a add_tag_value
> and go to the next sequence and called again add_tag_value creates two
> tags and so on.

But aren't you creating a new SeqFeature::Generic each time?  I don't
understand why you'd be reusing the same one over and over?

> I felling that using SeqFeature::Generic is wrong. But I'm really
> confused with Tools:GFF and SeqFeature::Generic in both modules you can

To clarify:

Bio::Tools::GFF is probably badly named -- it is just and Input/Output
mechanism for Bio::SeqFeatureI objects and GFF format. You can think of it
as analagous to Bio::SeqIO which reads/writes sequence formats,
Bio::Tools::GFF reads/writes feature formats (which don't have any
sequence).  We could theoretically write a Bio::SeqIO::gff which created a
sequence  which is empty but had a set of features attatched to it.


Bio::SeqFeature::Generic is the holder for the sequence feature data.


> manipulate a GFF and I couldn't choose between. This is sometimes
> frustrating I know I can do using Bioperl but I can't figure out how to
> do it.
>
>
> Marco.
>
>
> Jason Stajich wrote:
> > It is a little more flexible to do:
> >
> > use Bio::Tools::GFF;
> > my $io = new Bio::Tools::GFF(-file => '>filename');
> >       # defaults to STDOUT if no -file or -fh is provided
> > $io->write_feature($feat);
> >
> >
> > No way to change a tag though without violating the API (going under
> > the hood -- which you CAN do, we just don't recommend it) - are you sure
> > that is what you want to do?  Seems strange to be updating a tag's value
> > constantly but you must have a specific reason?
> >
> > -jason
> >
> > On Tue, 27 Aug 2002, Marco Aurelio Valtas Cunha wrote:
> >
> >
> >>Hi Bioperl,
> >>
> >>I don't think this is the better way to do it, but...
> >>I'm using SeqFeature::Generic to create a GFF2 output, some like this:
> >>
> >>#!/usr/bin/perl
> >>
> >>my $gff_io = new Bio::SeqFeature::Generic();
> >>
> >>--cut--
> >>
> >># Some loop ...
> >>
> >>$gff_io->add_tag_value("Target","Sequence:$query");
> >>
> >>        print $gff_io->gff_string();
> >>
> >>$gff_io->remove_tag("Target");
> >>
> >>#end of the loop;
> >>
> >>
> >>The issue is that I always have to add_tag_value() and then
> >>remove_tag(), cause AFAIK there's no way to change the tag value once is
> >>created, am I right? or there's a better way to do this?
> >>
> >>Thank you,
> >>Marco Valtas.
> >>
> >>
> >>
> >
> >
>
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu