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

[Marco Aurelio Valtas Cunha]

Hi Lincoln,

Yes I'm doing this now, and I think, I won a couple of runtime seconds. 
I have the script waiting for moderator approval, if it gets in then you 
can see what I'm doing now.

This confusion about how to use SeqFeature comes from a concept that I 
have in mind that instanciate an object is always a heavy task. so I try 
to avoid it, but I really don't know if this a real concern that I 
should have.

Marco.



Lincoln Stein wrote:
> 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.
>>>>>
> 
> 


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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
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email: mavcunha@bit.fmrp.usp.br