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

Mark Johnson johnsonm at gmail.com
Tue Jul 17 14:23:58 EDT 2007


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?


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