[Bioperl-l] xyplot glyph problem with previous aggregation
Luis A. M. Quintales
lamq at usal.es
Thu Apr 10 15:52:24 UTC 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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