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

Heikki Lehvaslaiho heikki at sanbi.ac.za
Thu Jun 8 04:52:27 EDT 2006


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
>
>
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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