<div dir="ltr">Hi Stuart,<div><br></div><div>It should work, yes.</div><div><br></div><div>Can you give me a snippet of your file to test on?</div><div><br></div><div>Thanks</div><div><br></div><div>Will</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On 22 May 2013 14:04, Stuart Meacham <span dir="ltr"><<a href="mailto:sm766@cam.ac.uk" target="_blank">sm766@cam.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Will,<br>
<br>
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?<br>
<br>
Thanks<br>
<br>
Stuart<div class="im"><br>
<br>
On 20/05/13 13:31, Will McLaren wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Hi Stuart,<br>
<br>
We provide a script for doing similar:<br>
<br>
ensembl-variation/scripts/<u></u>misc/convert_ensembl_to_SO_<u></u><a href="http://consequences.pl" target="_blank">consequences.pl</a><br>
<br>
You can also manually pull in the data from the %Bio::EnsEMBL::Variation::<u></u>Utils::Constants::OVERLAP_<u></u>CONSEQUENCES hash.<br>
<br>
Regards<br>
<br>
Will<br>
<br>
<br>
<br>
<br></div><div class="im">
On 20 May 2013 13:13, Stuart Meacham <<a href="mailto:sm766@cam.ac.uk" target="_blank">sm766@cam.ac.uk</a> <mailto:<a href="mailto:sm766@cam.ac.uk" target="_blank">sm766@cam.ac.uk</a>>> wrote:<br>
<br>
Hi,<br>
<br>
I have a database table on which I need to convert my Ensembl<br>
consequence 'strings' to SO consequence strings using the<br>
information here:<br>
<br>
<a href="http://www.ensembl.org/info/docs/variation/predicted_data.html#consequences" target="_blank">http://www.ensembl.org/info/<u></u>docs/variation/predicted_data.<u></u>html#consequences</a><br>
<br>
Is there any reason that the table in the above page shows the<br>
database strings (i.e. unicase with spaces replaced by underscore)<br>
for SO consequence and human readable strings (i.e. those that<br>
were actually displayed on the website) for the Ensembl<br>
consequence? Showing the same type of data for both fields would<br>
be very helpful ;)<br>
<br>
Thanks<br>
<br>
Stuart<br>
<br>
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