[ensembl-dev] Consequences: Ensembl -> SO

Will McLaren wm2 at ebi.ac.uk
Mon May 20 13:31:51 BST 2013


Hi Stuart,

We provide a script for doing similar:

ensembl-variation/scripts/misc/convert_ensembl_to_SO_consequences.pl

You can also manually pull in the data from the
%Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES hash.

Regards

Will




On 20 May 2013 13:13, Stuart Meacham <sm766 at cam.ac.uk> wrote:

> Hi,
>
> I have a database table on which I need to convert my Ensembl consequence
> 'strings' to SO consequence strings using the information here:
>
> http://www.ensembl.org/info/**docs/variation/predicted_data.**
> html#consequences<http://www.ensembl.org/info/docs/variation/predicted_data.html#consequences>
>
> Is there any reason that the table in the above page shows the database
> strings (i.e. unicase with spaces replaced by underscore) for SO
> consequence and human readable strings (i.e. those that were actually
> displayed on the website) for the Ensembl consequence? Showing the same
> type of data for both fields would be very helpful ;)
>
> Thanks
>
> Stuart
>
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