[Bioperl-l] <no subject>

Lincoln Stein lstein at cshl.edu
Mon Mar 6 10:47:21 EST 2006


By the way, you'll want to CVS update to the latest bioperl live code in order 
to parse the flybase gff3 files correctly.

Lincoln

On Monday 06 March 2006 00:02, Marco Blanchette wrote:
> Dear all--
>
> I am trying to forge my first bioperl weapons with the
> Bio::DB::GFF and Bio::Graphics modules. My goal is to display genes with
> their underlying mRNAs and later on add addition useful info (ie binding
> site for our preferred proteins).
>
> I loaded the GadFly gff3 annotation in a mysql database using
> bulk_load_gff.pl and I am trying to pass a Bio::SeqFeatureI to the
> Bio::Graphics::add_feature method.
>
> My understanding is that:
> my $tcs = $tg->features(-types =>'processed_transcript',
>                                         -attributes => {Parent => $gene},
>                                         -iterator => 1);
>
> Produces a Bio::SeqIO object that can be iterate through the next_seq
> method to get a Bio::Seq object that could be used to extract a
> Bio::SeqFeatureI by using the get_SeqFeatures method.
>
> Somehow, my script does not produce the expected results. Could somebody
> put me on back on the right track.
>
>
> #!/usr/bin/perl
> use strict;
> use warnings;
> use Bio::DB::GFF;
> use Bio::Graphics;
>
> my $dmdb = Bio::DB::GFF->new( -adaptor => 'dbi::mysql',
>                                    -dsn => "chr4",
>                                    );
>
>
> my @genes = ('CG2041'); ##a gene on the fourth chromosome
>
> foreach my $gene (@genes){
>
>     my $geneseg = $dmdb->segment(-name => $gene, -merge);
>
>     if ($geneseg){
>
>     my @tgs = $geneseg->features(-types => 'gene');
>
>     for my $tg (@tgs){
>
>         my $length = $tg->length();
>
>         my $panel = Bio::Graphics::Panel->new(-length => $length, -width 
> => 800);
>
>         my $track = $panel->add_track(    -glyph => 'generic',
>                                         -label  => 1);
>
>         my $tcs = $tg->features(-types =>'processed_transcript',
>                                         -attributes => {Parent => $gene},
>                                         -iterator => 1);
>
>         while ( my $tc = $tcs->next_seq ){
>             $track->add_feature($tc->get_SeqFeatures);
>         }
>
>         print $panel->png;
>     }
> }
> }
>
> Many thanks
>
>
> Marco Blanchette, Ph.D.
>
> mblanche at berkeley.edu
>
> Donald C. Rio's lab
> Department of Molecular and Cell Biology
> 16 Barker Hall
> University of California
> Berkeley, CA 94720-3204
>
> Tel: (510) 642-1084
> Cell: (510) 847-0996
> Fax: (510) 642-6062
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
FOR URGENT MESSAGES & SCHEDULING, 
PLEASE CONTACT MY ASSISTANT, 
SANDRA MICHELSEN, AT michelse at cshl.edu


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