RE: Greek characters
2009-05-05 23:03:52 GMT
Sorry I didn't cc you with my replies to James. Please see below:
Hi James, Thanks for the suggestion. I've tried this in Safari and Firefox now, and both give identical results either using the default character set or forcing UTF-8: the alpha character is returned as capital I hat plus/minus in all cases.
In command line, using SELECT through mysql or using Syed's suggestion of scripts/webExample.pl both return an alpha character correctly.
I also tried pasting the gene name with the alpha character in as a filter. In this case, the alpha character shows up correctly in the filter panel in the left window of martview, but no records are returned.
Further to using the gene name with the alpha character as a filter, I though you might be interested in how it looks in the XML query.
In the previous case (returning a value from the database containing the alpha character) it was displayed in martview as capital-I-hat plus-minus (two characters). In the case of using the alpha character as a filter and looking at the resulting XML query, it shows as capital-A-tilde capital-Z-accent capital-A-hat plus-minus (4 characters).
Dr. Jonathan Moore
Senior Research Fellow in Bioinformatics
Warwick Systems Biology Centre
University of Warwick
Coventry CV4 7AL
+44 (0)24 761 50332
From: Syed Haider [mailto:syed <at> ebi.ac.uk]
Sent: Sat 5/2/2009 11:04 AM
To: Moore, Jonathan
Cc: James Smith; mart-dev <at> ebi.ac.uk
Subject: Re: [mart-dev] Greek characters
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.
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
> +44 (0)24 761 50332
> -----Original Message-----
> From: James Smith [mailto:js5 <at> sanger.ac.uk]
> Sent: Tue 4/21/2009 2:30 PM
> To: Syed Haider
> Cc: Moore, Jonathan; mart-dev <at> ebi.ac.uk
> 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 Î± (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...
> >> (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/
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
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