[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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