I have alittle program that try to connect to a database with this f... module and structure called Bio::DB::GFF.
#!/usr/bin/perl
use strict;
use Bio::DB::GFF;
my $db = Bio::DB::GFF->new(-user => 'bio',
-pass => 'bio',
-dsn => 'elegans',
-aggregators => 'gene_model{coding_exon,5_
+UTR,3_UTR/CDS}');
my $gene_stream = $db->get_seq_stream('gene_model:curated');
while (my $gene = $gene_stream->next_seq) {
print $gene->name,"\n";
for my $part ($gene->get_SeqFeatures) {
print "\t",join("\t",$part->method,$part->start,$part->end),"\n";
}
print "\n";
}
When I execute it, i have this error:
2L52.1
------------- EXCEPTION Bio::Root::NotImplemented -------------
MSG: Abstract method "Bio::FeatureHolderI::get_SeqFeatures" is not imp
+lemented by package Bio::DB::GFF::Feature.
This is not your fault - author of Bio::DB::GFF::Feature should be bla
+med!
Any Idea / suggestion monks?
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