[ensembl-dev] Consequences: Ensembl -> SO

[Will McLaren]

Hi Stuart,

It should work, yes.

Can you give me a snippet of your file to test on?

Thanks

Will


On 22 May 2013 14:04, Stuart Meacham <sm766 at cam.ac.uk> wrote:

> 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<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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