[ensembl-dev] Consequences: Ensembl -> SO

[Stuart Meacham]

Hi Will,

I used this script on a MySQL database dump of a table containing a 
field of old Ensembl consequences. The script ran without error but no 
consequences were altered. Does the input 'text' file need to be 
formatted or would you expect this to have worked?

Thanks

Stuart

On 20/05/13 13:31, Will McLaren wrote:
> 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 
> <mailto: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
>
>     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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