[Bioperl-l] parsing GenScan result

[Yanbin Yin]

Brain and Jason,

Thank you for your reply.

Using the following script I could get the exons' coordinates, but I still do not know how to get the exon sequence.

use Bio::Tools::Genscan;
my $genscan = Bio::Tools::Genscan->new(-file => "$filename");
while($gene = $genscan->next_prediction()) {
    @exon_arr = $gene->exons();
    foreach my $exon(@exon_arr) {
        my $start = $exon->start();
        my $end = $exon->end();
    }
}

I checked the object Bio::Tools::Prediction::Exon, its method $predicted_cds_dna = $exon->predicted_cds() doesn't work. How come?

Yanbin


----- Original Message ----- 
From: "Brian Osborne" <brian_osborne at cognia.com>
To: "Jason Stajich" <jason at cgt.duhs.duke.edu>; "Yanbin Yin" <yinyb at mail.cbi.pku.edu.cn>
Cc: <bioperl-l at bioperl.org>
Sent: Thursday, July 01, 2004 2:36 AM
Subject: RE: [Bioperl-l] parsing GenScan result


> Yanbin,
> 
> What Jason is saying is that the Synopsis is telling you that
> Bio::Tools::Prediction::Gene objects are returned, for example. So you'll
> need to go that module's documentation and see how to get the appropriate
> information from that object.
> 
> Brian O.
> 
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jason Stajich
> Sent: Wednesday, June 30, 2004 1:49 PM
> To: Yanbin Yin
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] parsing GenScan result
> 
> did you try the SYNOPSIS part of the documentation from
> Bio::Tools::Genscan?
> 
> Also see the bptutorial.pl which has a genscan example.
> 
> -jason
> On Thu, 1 Jul 2004, Yanbin Yin wrote:
> 
> > Hi,
> >
> > I am trying to parse GenScan prediction result. I found one example script
> written by Brian Osborne. It is very good but I still want to parse out each
> exon's sequence and location. Had anyone written this kind of script or
> could anyone please tell me how to use Bio::Tools::Genscan to write one?
> >
> > Thanks in advance!
> >
> > Yanbin
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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> 
>