[Bioperl-l] [Gmod-schema] beginning work on SeqIO::chadoxml

Chris Fields cjfields at uiuc.edu
Fri Feb 2 11:37:49 EST 2007


I was going to suggest maybe allowing one to switch out XML handlers/ 
writers based on the style (ala XML::SAX), but I see that chadoxml  
currently uses XML::Writer and there is no next_seq() implemented.   
Oh well...

chris

On Feb 2, 2007, at 10:03 AM, Scott Cain wrote:

> Hi Hilmar,
>
> That is a good idea; when I started down this road, it felt like there
> would only be a few things that I might want to allow to be different,
> but I think you are right that having one standard implementation that
> can be subclassed for legacy systems is a good thing.
>
> Scott
>
>
> On Fri, 2007-02-02 at 10:09 -0500, Hilmar Lapp wrote:
>> On Feb 1, 2007, at 2:55 PM, Scott Cain wrote:
>>
>>> The second main change was to introduce a -flybase_compat argument
>>> when
>>> initializing the Bio::SeqIO writer, so that 'old style' cv and  
>>> cvterms
>>> (that are compatable with flybase) will be used, but now the default
>>> will be to use current standards:
>>
>> Just my $0.02 ... obviously, Flybase may be the only organization
>> that uses an 'old style' or any other way not compliant with 'current
>> standards' (presumably SO), but if it's not the only one then this
>> approach won't scale.
>>
>> Also, an argument -flybase_compat suggests to the unsuspecting that
>> this is an endorsed flavor of the standard and fine to use for
>> everyone else too.
>>
>> If Flybase is idiosyncratic in this way, why not make chadoxml.pm
>> compliant with the standard as we all want it, keep it free from
>> litter caused by usage of old versions of SO, and create a second
>> module fb-chadoxml.pm that inherits from the first and merely
>> overrides a few things so that it works for Flybase. This way, other
>> organizations with similar needs can follow the path and create their
>> own xyz-chadoxml.pm, rather than having to muck around in the
>> chadoxml.pm that comes with the distribution.
>>
>> I'm not sure I fully grasp the underlying issue, so I may not make
>> much sense here. Apologies if that's the case ...
>>
>> 	-hilmar
> -- 
> ---------------------------------------------------------------------- 
> --
> Scott Cain, Ph. D.                                    
> cain.cshl at gmail.com
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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