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

[Marco Aurelio Valtas Cunha]

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
 >
 > _______________________________________________
 > Bioperl-l mailing list
 > Bioperl-l@bioperl.org
 > http://bioperl.org/mailman/listinfo/bioperl-l
 >
 >


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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