[Bioperl-l] Bio::ClusterIO::dbsnp broken in bioperl-live
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.
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.
> On Wednesday 07 June 2006 21:38, Chris Fields wrote:
>> Don't know how many people use Bio::ClusterIO this module, but it
>> 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:
>> 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
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