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

[Marco Aurelio Valtas Cunha]

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


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Marco Aurélio Valtas Cunha
Laboratório de Bioinformática
Hemocentro de Ribeirão Preto
Faculdade de Medicina de Ribeirão Preto
Universidade de São Paulo
Tel 55 16 3963-9300 R: 9603
http://bit.fmrp.usp.br
http://scarecrow.fmrp.usp.br/~mavcunha/public/
email: mavcunha@bit.fmrp.usp.br