[Bioperl-guts-l] [Bug 2018] Bio::ClusterIO::dbsnp breaks with new XML output

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Mar 7 17:10:57 EST 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2018


ahawkins at watson.wustl.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|allenday at ucla.edu           |
              Alias|                            |ahawkins
             Status|RESOLVED                    |REOPENED
         Resolution|FIXED                       |




------- Comment #4 from ahawkins at watson.wustl.edu  2007-03-07 17:10 EST -------
It looks like dbSNP has changed their xml format again, causing
Bio::ClusterIO::dbsnp tests to fail. The latest dbSNP xml files (version 126)
are found at ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/XML/ (compare
gunzip ds_chY.xml.gz vs Bio/t/data/LittleChrY.dbsnp.xml).

The first obvious issue is that the regexp in next_cluster() (in lines 184 and
186 of Bio::ClusterIO::dbsnp) now needs to match on "<Rs" not "<Rs>". After
making this change, however, next_cluster() returns only a skeleton
Bio::Variation::SNP object, with no useful data in it. 

Has anyone looked at this?


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