[ensembl-dev] looking up GENSCAN transcripts?

Ian Sealy is1 at sanger.ac.uk
Sun Oct 2 20:33:41 BST 2011

Dear Janet,

> I could use a little help on the perl API, I'm afraid.
> I've been using the perl API to pull out exon coordinates for 
> transcripts from various species.  I can make it work fine for 
> transcripts in the 'cdna' set (e.g. ENSCAFT00000018598) but I can't 
> make it work for ab initio transcripts (e.g. GENSCAN00000055763).  I 
> pulled out some ab initio transcript IDs I'm interested in by 
> downloading the full set and blasting with some genes I'm interested 
> in.
> I'm know my problem is probably one of the following:
> 	wrong adaptor group
> 	wrong adaptor type
> 	wrong method (do I have a stable ID or some other kind of ID?)
> But I'm not sure which one, and I'm not sure how to proceed to figure it out.
> The script I was trying is shown below.  Any suggestions appreciated.

Ab initio predictions are PredictionTranscript objects, not Transcript 
objects. So try changing:

my $tx_adaptor2 = $registry->get_adaptor('canis_familiaris', 'Core', 'Transcript');


my $tx_adaptor2 = $registry->get_adaptor('canis_familiaris', 'Core', 'PredictionTranscript');


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