[Bioperl-l] Bio::OntologyIO problems

[James Mitchell]

I have been having problems with the latest files that I've downloaded from 
geneontology.org.  I use bioperl to parse these files and when I use the new 
files, I get an error from bio-perl now.  Using GO files dated July 15, the 
parsing works.

Any help or suggestions?

This is the call I use in bioperl-1.4.

my $deffile = "GO.defs";
my $comfile = "component.ontology";
my $funfile = "function.ontology";
my $profile = "process.ontology";

my $ont_stream = Bio::OntologyIO->new(-format => 'go',
                                         -files =>  [$comfile,
										$funfile,
										$profile],
                                         -defs_file => $deffile);

$engine = $ont_stream->next_ontology();

This is the error I receive with the new GO files:

------------- EXCEPTION  -------------
MSG: format error: no term id in line ":0017023
"
STACK Bio::OntologyIO::dagflat::_get_first_termid 
C:/Perl/site/lib/Bio/OntologyI
O/dagflat.pm:600
STACK Bio::OntologyIO::dagflat::_parse_flat_file 
C:/Perl/site/lib/Bio/OntologyIO
/dagflat.pm:472
STACK Bio::OntologyIO::dagflat::parse 
C:/Perl/site/lib/Bio/OntologyIO/dagflat.pm
:250
STACK Bio::OntologyIO::dagflat::next_ontology 
C:/Perl/site/lib/Bio/OntologyIO/da
gflat.pm:284
STACK MostInformative::find MostInformative.pm:96
STACK toplevel MostInformative.pl:75

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