[ensembl-dev] slice adaptor

Hardip Patel H.Patel at victorchang.edu.au
Fri Oct 8 05:07:03 BST 2010

Hi all

I am using ensembl api to extract information for overlapping features to the regions of interest. here is the code that I am using.

my $start = shift;
my $end = shift;
my $chr = shift;
my $strand = shift;

my $slice_adaptor = $registry->get_adaptor('mouse', 'Core', 'slice');
my $coordinate_system = "chromosome";

my $slice = $slice_adaptor->fetch_by_region($coordinate_system, $chr, $start, $end, $strand, 'NCBIM37');

print $slice->seq_region_name ." is chromosome and ".$slice->seq_region_length ." is length\n";

I have tried using the fetch_by_region method with and without one/all of the following:
$coordinate_system, strand and version.

I have always supplied $chr $start and $end as at the minimum three arguments to method call.

When I check the seq_region_name it corresponds with the chromosome name I supply.
However, the seq_region_length doesn't correspond to the start and end I supply. instead it just returns the slice over the whole chromosome.

Can somebody please let me know if I am doing something wrong or not?


Hardip R. Patel
Bioinformatician, Molecular Genetics Division,
Victor Chang Cardiac Research Institute,
Darlinghurst, NSW - 2010, Australia
(W): +61 - 2 - 9295 8611
(M): 0449 180 715

VCCRI 12th International Symposium
"Charting the depths of RNA: from molecules to therapies"
19 November 2010
visit http://www.victorchang.edu.au for details

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