[Bioperl-l] parsing GenScan result

[Brian Osborne]

Yanbin,

I'll add this code to the example script. Thank you.

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 Yin Yanbin
Sent: Thursday, July 01, 2004 7:53 AM
To: Brian Osborne
Cc: Bioperl
Subject: Re: [Bioperl-l] parsing GenScan result
Importance: High

Brian,

I added the following codes in your GenScan example parser. Now it can print
out the exon sequence.

Thank you.

   my @exon_arr = $gene->exons;
   my $i = 1;
   foreach my $exon (@exon_arr) {
    print EXON ">".$id."_".$1."_EXON_".$i." ".$exon->strand."
".$exon->start."|".$exon->end."\n".$seq->subseq($exon->start,
$exon->end)."\n";
    $i++;
   }


Yanbin
_________________________________________________________

Yanbin(Benjamin) Yin, Ph.D. Student
Center of Bioinformatics (CBI),
College of Life Sciences,
Room 607, New Life Science Building,
Peking University, 100871
Beijing, P.R.China

Tel: 86 10 6275 6730
E-mail: yinyb at mail.cbi.pku.edu.cn



----- 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
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