[ensembl-dev] retrieving sequence data from previous assemblies using fetch_by_region method

Duarte Molha duartemolha at gmail.com
Mon Oct 6 17:23:36 BST 2014


Dear developers

I have the latest API downloaded and I would want to create a scritp that
could retrieve sequence information from a specified assembly

so I have made a script that tries to accomplish this:

so ...assuming this coordinates:

chr: 5
from: 112043202
to: 112046226
strand = 1
assembly = GRCh38

    my $slice = $slice_adaptor->fetch_by_region( 'chromosome', $chrom,
$from, $to, $strand, $assembly );


        $seq        = $slice->seq();

I can retrieve the dna sequence:

>CHR5-112043202-112046226       chr5:112043202-112046226
AGTATATAATCACAT..............CTAAAAGCAAACA


However, if I give it the variables:

chr: 5
from: 112043202
to: 112046226
strand = 1
assembly = GRCh37 or NCBI36

i get :

>CHR5-112043202-112046226       chr5:112043202-112046226
NNNNNNNNN.........NNNNNNNNNNNNNNNN


How can I get the correct underlying sequence?

Best regards

Duarte
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