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

[Marco Aurelio Valtas Cunha]

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.
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
> 


-- 
##############################################################
# Atenção meu email mudou para  mavcunha@bit.fmrp.usp.br     #
# Veja porque http://scarecrow.fmrp.usp.br/~mavcunha/public  #
# Attention my email changed to mavcunha@bit.fmrp.usp.br     #
# See why here http://scarecrow.fmrp.usp.br/~mavcunha/public #
##############################################################
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