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

[Lincoln Stein]

Hi Marco,

Probably better to create one Bio::SeqFeature::Generic each time, and then to 
call its gff_string() method:

$f = Bio::SeqFeature::Generic->new( -seqname=>'Chr10',
						-start => 10, 
						-end => 100,
						-score=>1000,
						-tag=>{Target=>'Sequence:fred 1 1000'});
print $f->gff_string;

Lincoln

On Wednesday 28 August 2002 10:56 am, Marco Aurelio Valtas Cunha wrote:
> Jason,
>
> Reusing the SeqFeature was was the mistake now I'll create a new
> SeqFeature each time.
>
> Thanks
> Marco.
>
> Jason Stajich wrote:
> > 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.