[Bioperl-l] Bio::DB::GFF problem

[Matthias Wahl]

  Hi Lincoln,

Thank you very much for your input. The $gff_db->segment call now works 
fine.

However, I am still not able to generate an xyplot. Using the following 
GFF file:

1    chromosome    Component    1    195869683    .    .    .    
Sequence "1"
1    EnsEMBL    gene_density    1    200000    0    .    .    
gene_density "1.density"
1    EnsEMBL    gene_density    200001    400000    0    .    .    
gene_density "1.density"
1    EnsEMBL    gene_density    400001    600000    0    .    .    
gene_density "1.density"
1    EnsEMBL    gene_density    600001    800000    0    .    .    
gene_density "1.density"
1    EnsEMBL    gene_density    800001    1000000    0    .    .    
gene_density "1.density"
1    EnsEMBL    gene_density    1000001    1200000    0    .    .    
gene_density "1.density"
...

I tried to aggregate all gene_density features

  my $aggregator = Bio::DB::GFF::Aggregator->new(-method    => 'density'
                                            
                                            -sub_parts => 'gene_density');

  my $gff_db = Bio::DB::GFF->new(-adaptor =>'dbi::mysqlopt',
                                                            
-dsn=>'dbi:mysql:Mus_musculus_GFF',
                                                            -user => 
'XXXXX',
                                                            -pass => 'XXXXX,
                                                            -aggregator 
=> $aggregator,
                                                            );
  my $gene_density = $gff_db->segment($chromosome_name) or die "Can not 
retrieve GFF segment: ".$gff_db->error;
  my @features = $gene_density->features('gene_density');

This all works fine. But when I try to draw a xyplot

  $picture->add_track(\@features,
                      -glyph => 'xyplot');

I end up with bars in my image, but no plot!

Could you by chance tell me what I am doing wrong?

Many thanks

Matthias



Lincoln Stein wrote:

>Hi,
>
>I'm catching up on my bioperl mail after being on vacation for August.  The 
>problem is that you need an entry for the whole chromosome because the 
>segment() call needs to retrieve it in order to get the length.  Something 
>like this will do the trick:
>
>1 EnsEMBL chromosome 1 1502911 . . . Chromosome 1
>
>Lincoln
>
>On Wednesday 13 August 2003 07:02 pm, Matthias Wahl wrote:
>  
>
>>Hi all!
>>
>>I have trouble in using Bio::DB::GFF with the following code:
>>
>>my $aggregator = Bio::DB::GFF::Aggregator->new(-method    => 'gene_density'
>>                                               -sub_parts =>
>>'EnsEMBL:gene_density');
>>
>>my $gff_db = Bio::DB::GFF->new(-adaptor =>'dbi::mysqlopt',
>>                               -dsn=>'dbi:mysql:Mus_musculus_GFF',
>>                               -user => 'xxxxx',
>>			       -pass => 'xxxxx',
>>			       -aggregator => $aggregator
>>			       );
>>
>>
>>Calling
>>
>>$gff_db->segment(-class=>'Chromosome',
>>                 -value=>'1');
>>
>>always returns undef (whatever arguments I use)!
>>The database has been generated by loading a GFF file of the following
>>format:
>>
>>1	EnsEMBL gene_density    1000001 2000000 0                      
>>Chromosome 1
>>
>>1       EnsEMBL gene_density    2000001 3000000 0                      
>>Chromosome 1
>>
>>1       EnsEMBL gene_density    3000001 4000000 1                      
>>Chromosome 1
>>
>>1       EnsEMBL gene_density    4000001 5000000 12                     
>>Chromosome 1
>>
>>1       EnsEMBL gene_density    5000001 6000000 4                      
>>Chromosome 1
>>
>>with load_gff.PLS (columns are tab-seperated, the 9th column consists of
>>'Chromosome' and name, seperated by space), both with and without the
>>associated sequence file.
>>
>>Calling
>>
>>$gff_db->features()
>>
>>works fine. But I need aggregated features for generating a
>>Bio::Graphics xyplot (to plot the gene density for a particular
>>chromosome).
>>
>>Many thanks,
>>
>>Matthias
>>    
>>
>
>  
>

-- 
Matthias Wahl
GSF-National Research Center for Environment and Health
Institute of Developmental Genetics
Ingolstaedter Landstrasse 1
D-85764 Neuherberg
Germany
TEL: ++49 89 3187-4117,-2638
FAX: ++49 89 3187-3099
E-mail: matthias.wahl at gsf.de
WWW: http://www.gsf.de/idg