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/ >> -- 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 office is 215 Euston Road, London, NW1 2BE.
