[ensembl-dev] Bio::EnsEMBL::Slice::expand

[Andy Yates]

Hi Ben

The expand code is strand aware so your first param is always 5 prime and second is 3 prime. However if you have a gene asking for its slice will return the Slice the feature is located on in the forward orientation i.e. the chromosome. To get the strand aware slice use feature_Slice and then call expand.

Hope this helps,

Andy

On 28 Mar 2012, at 13:35, Benoît Ballester <benoit at ebi.ac.uk> wrote:

> Hi,
> 
> I have a question regarding the $slice->expand method.
> 
> Could you confirm that if the gene is on the -1 strand and I want to expand the upstream region of this gene I need to write my code like this :
> 
> $slice = $gene->slice->expand('', $ext5) if (strand < 0)
> $slice = $gene->slice->expand($ext5, '') if (strand > 0)
> 
> Thanks, 
> 
> Ben
> 
> 
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