[Bioperl-l] xyplot glyph problem with previous aggregation

Luis A. M. Quintales lamq at usal.es
Thu Apr 10 11:52:24 EDT 2008


I am not able to add xyplot glyphs to one panel because I have some
problems with the aggregations.

Using that GFF file:

##sequence-region chr1 1 5578650
chr1  atfreq  atpc    1  50   58.8000   .  .  atpc 1
chr1  atfreq  atpc   51 100   58.4000   .  .  atpc 1
chr1  atfreq  atpc  101 150   57.6000   .  .  atpc 1
chr1  atfreq  atpc  151 200   57.8000   .  .  atpc 1
. . .


And this source code for preparing the aggregated features necessary for
the xyplot glyph:

my $filin  = $ARGV[0];
my $db = Bio::DB::GFF->new( -dsn => $filin,
                            -adaptor => 'memory',
                            -aggregator => 'at{atpc:atfreq}'
                           );
my $segment  = $db->segment('chr1');
my @features1 = $db->features('atpc');
print "$#features1 \n";
my @features2 = $segment->features('atpc');
print "$#features2 \n";
my @features3 = $db->features('at');
print "$#features3 \n";
my @features4 = $segment->features('at');
print "$#features4 \n";

I obtain:

111572
111572
0
0

What I am doing wrong with the aggregator?

Many thanks.




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