[Bioperl-l] Should Bio::SeqIO::interpro 'use XML::DOM::XPath'?
Mark Johnson
johnsonm at gmail.com
Tue Jul 17 18:23:58 UTC 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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