[ensembl-dev] getting gene exons and transcripts that overlap only the original slice

[Andrea Edwards]

Hello

i have this code below taken from the core api tutorial which gets me 
all the exons and transcripts for the gene(s) that overlap a slice.

  I was hoping for an easy way to get those features of the gene that 
only overlap the original one bp slice; this code gets all exons and 
transcripts
associated with the gene

I thought you might be able to call 'get_all_Object' methods with a 
parameter which represents a region of sequence overlap but it seems not.
I also thought they might be filtered automatically based on the 
underlying slice but it seems not.

Naturally i can filter the features in the list based on their start and 
end positions but for speed it would be easier not to retrieve them all at.
I have a lot of data so speed is important. Please can you advise the 
best way to do this.

$slice = $slice_adaptor->fetch_by_region( 'chromosome', '9', 21816758,  
21816758 );

my $genes = $slice->get_all_Genes();
while ( my $gene = shift @{$genes} ) {
     my $gstring = feature2string($gene);
     print "$gstring\n";

     my $transcripts = $gene->get_all_Transcripts();
     while ( my $transcript = shift @{$transcripts} ) {
         my $tstring = feature2string($transcript);
         print "\t$tstring\n";

         foreach my $exon ( @{ $transcript->get_all_Exons() } ) {
             my $estring = feature2string($exon);
             print "\t\t$estring\n";
         }
     }
}

print "done\n";

Many thanks