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

[Lincoln Stein]

You might also look at Heikki's Bio::Coordinate mapper. See the code at the 
bottom of t/CoordinateMapper.t to see how it works.

Lincoln

On Wednesday 28 August 2002 03:01 pm, Marco Aurelio Valtas Cunha wrote:
> I've got this message stuck on moderator approval cause the attachment,
> so here is without the attachment, maybe later the other gets in.
>
> Hi Hilmar,
>
> I avoid post scripts to not load you guys, cause I know that everybody
> is working and when there's a time you respond to the list.
>
> Probably you won't be able to run this script cause will be missing some
> files, but in short what I try to do is:
>
> Data: A megablast result (Human NT contigs vs 900K ESTS) and a DB::GFF
> (human mapview information from NCBI)
>
> First problem is that GFF format is not a hierarchical format, so if I
> blasted with NT then I need retrieve the position of the NT on the
> Chromosome so I can discover the position of my ESTs on the chromosome.
>
> Then I parse the megablast using Bonnie module MBPlite.pm, with DB::GFF
> ( and a help from Lincoln Stein) I convert blast coordenates to absolute
> coordenates so I can save the GFF file with the right information, and
> this file will be uploaded to my MySQL (DB::GFF) database.
>
> To do all I use Bioperl, but I'm little experienced on Bioperl so
> sometimes I choose not the best way to solve my problems.
>
> Marco.
>
> Hilmar Lapp wrote:
>  >>-----Original Message-----
>  >>From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
>  >>Sent: Wednesday, August 28, 2002 7:32 AM
>  >>To: Marco Aurelio Valtas Cunha
>  >>Cc: Bioperl
>  >>Subject: Re: [Bioperl-l] Tag handling on SeqFeature::Generic
>  >
>  > [...]
>  >
>  >>>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.
>  >
>  > In fact internally calling $seqfeature->gff_string() delegates to an
>
> instance of Bio::Tools::GFF to do the job. So there's really no
> difference between the output.
>
>  > Bio::Tools::GFF is indeed badly named -- it should be in a
>
> Bio::SeqFeatureIO directory to be consistent with Bioperl's other IO
> module layouts.
>
>  > Marco, if you want comments on how you accomplished the job in your
>
> script you should post the script, or its relevant parts.
>
>  > 	-hilmar
>  >
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