Hi Jonathan,
apologies for the delay, i guess i missed some emails on this. Did the
trick James proposed, browser charset settings worked ???
I remember, you mentioned for the XML query in shell, the characters
were printed just fine.
thanks
Syed
Moore, Jonathan wrote:
Hi James and Syed,
Any advance on the character set issue?
Dr. Jonathan 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://www.warwick.ac.uk/go/jaymoore
-----Original Message-----
From: James Smith [mailto:[email protected]]
Sent: Tue 4/21/2009 2:30 PM
To: Syed Haider
Cc: Moore, Jonathan; [email protected]
Subject: Re: [mart-dev] Greek characters
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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