[Bioperl-l] Bio::ClusterIO::dbsnp broken in bioperl-live

Chris Fields cjfields at uiuc.edu
Thu Jun 8 08:56:27 EDT 2006


Sounds good to me.  If someone wants to use this down the line, they  
might be desperate enough to provide patches; there are a lot of  
commented out tags.

Chris

On Jun 8, 2006, at 3:52 AM, Heikki Lehvaslaiho wrote:

> I sort of fixed this.
>
> At least the tests pass (I commented out two) when using the new  
> sample XML.
> To be really usefull, the code need much more work, so I left the  
> bug open.
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2018
>
>
> 	-Heikki
>
>
> On Wednesday 07 June 2006 21:38, Chris Fields wrote:
>> All,
>>
>> Don't know how many people use Bio::ClusterIO this module, but it  
>> looks
>> like Bio::ClusterIO::dbsnp is broken unless you are using older XML
>> versions of the dbSNP database; the schema for ASN.1 and XML  
>> format for SNP
>> has changed:
>>
>> http://www.ncbi.nlm.nih.gov/projects/SNP/
>>
>> under 'Announcements'.
>>
>> I actually tried parsing the dbsnp test file and a newer schema  
>> XML file to
>> confirm this; the new version doesn't work (returned object from
>> next_cluster is undef).  I'm filing a bug as a reminder.
>>
>> Christopher Fields
>> Postdoctoral Researcher - Switzer Lab
>> Dept. of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>     _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
>    _/  _/  _/  SANBI, South African National Bioinformatics Institute
>   _/  _/  _/  University of Western Cape, South Africa
>      _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
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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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