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

Chris Fields cjfields at uiuc.edu
Wed Jun 7 15:38:08 EDT 2006


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 




More information about the Bioperl-l mailing list