[Bioperl-l] Should Bio::SeqIO::interpro 'use XML::DOM::XPath'?

Chris Fields cjfields at uiuc.edu
Tue Jul 17 17:04:44 EDT 2007


On Jul 17, 2007, at 1:23 PM, Mark Johnson wrote:

> I'm tinkering with parsing iprscan reports with BioPerl.  I noticed  
> that this:
>
>   my $seqio = Bio::SeqIO->new(-file => $iprscan_file, -format =>  
> 'interpro');
>
>   while (my $seq = $seqio->next_seq()) {
>       ...
>   }
>
> Does not work unless I first 'use XML::DOM::XPath'.  I get this error:
>
>   Can't locate object method "findnodes" via package
> "XML::DOM::Document" at
> bioperl-cvs/bioperl-live//Bio/SeqIO/interpro.pm line 136, <GEN0> line
> 30.
>
> I see that Bio::SeqIO has 'use XML::DOM', but that doesn't seem to
> suck in XML::DOM::Xpath.  I see that t/interpro.t requires
> XML::DOM::XPath:
>
> test_begin(-tests => 17,
>                 -requires_module => 'XML::DOM::XPath');
>
> Is suppose the reason the test specs a require XML::DOM::XPath is so
> that tests can be skipped if XML::DOM::XPath is not available.
> Shouldn't Bio::SeqIO::interpro 'use XML::DOM::XPath', though?

You're right; I think tests passed b/c XML::DOM::XPath (if present),  
was eval'd as a required module.  When I commented out the spot where  
it is eval'd in the test suite I can replicate this error.  I have  
added 'use XML::DOM::XPath' to SeqIO::interpro now in CVS and it  
passes fine.

Thanks for the heads up!

chris


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