Syed Haider wrote:
Hello Jonathan,
Before we embark on characterset fix, could you please do a little
test for us:
copy the XML equivalent of your query from MartView XML button. Paste
it into biomart-perl/scripts/Query.xml
edit biomart-perl/scripts/webExample.pl to point to your biomart server
now run:
perl webExample.pl Query.xml
from the shell and see what you get - alpha or I+- :)
thanks
Syed
Moore, Jonathan wrote:
Hello,
Sorry if this has been addressed but I couldn't find a reference in
the list archive.
We have a number of columns containing suggested gene names for our
organism which contain greek letters (alpha, beta, etc) as part of
the names. These are stored OK in the mart MySQL database, as I've
verified at the command line using mysql and SELECT... However,
martview is not showing them up correctly, for instance the alpha
character (?) is showing up as α (capital I hat plus/minus).
Now I understand a little of the basics of character sets, so I know
it is an ongoing bane, but is there a way to configure e.g. MySQL to
propagate this data correctly from back to front-end?
This looks like an encoding error biomart/martview is defaulting to
output in ISO-8859-1(or whatever your default charset is) the data is
stored in UTF-8, try in your browser forcing the character encoding...
(Firefox View -> Character encoding -> UTF-8) and see if you get the
right output...
James
(Regardless of whether this is a great idea, in terms of gene
nomenclature!)
Dr. Jay Moore
Senior Research Fellow in Bioinformatics
--
Warwick Systems Biology Centre
Coventry House
University of Warwick
Coventry CV4 7AL
U.K.
+44 (0)24 761 50332
http://www2.warwick.ac.uk/fac/sci/systemsbiology/
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Limited, a charity registered in England with number 1021457 and a
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