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

bugzilla-daemon at newportal.open-bio.org bugzilla-daemon at newportal.open-bio.org
Wed Jun 7 15:55:05 EDT 2006


           Summary: Bio::ClusterIO::dbsnp breaks with new XML output
           Product: Bioperl
           Version: main-trunk
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: cjfields at uiuc.edu

The dbSNP XML schema at NCBI has changed recently (Oct. 2005) (no longer uses
DTD).  Bio::ClusterIO::dbsnp breaks with new XML output from NCBI.

Using the old LittleChrY.dbsnp.xml (in t\data in bioperl-live), everything
works.  next_cluster returns a Bio::Variation::SNP object

Using the attached file (new XML) as input and using Data::Dumper as shown
below, get undef returned (probably should throw something instead here).  

test script
#! perl
use strict;
use warnings;
use Bio::ClusterIO;
use Data::Dumper;
my $cl_in = Bio::ClusterIO->new(-file => shift,
                               -format => 'dbsnp');

my $cl_out = Bio::ClusterIO->new(-fh    => \*STDOUT,
                                -format => 'unigene');
my $cluster = $cl_in->next_cluster;
print Dumper($cl_in);
print Dumper($cluster);

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