[Bioperl-guts-l] [Bug 2159] parsing xml blast results hit-description

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Dec 5 17:07:48 EST 2006


http://bugzilla.open-bio.org/show_bug.cgi?id=2159





------- Comment #7 from jcwang at cs.ucsd.edu  2006-12-05 17:07 -------
(In reply to comment #6)
> Using your script and data I get this:
> 
> hit name: gi|22026816|ref|NP_523836.2|
> hit desc: Adenylate kinase-2 CG3140-PA [Drosophila melanogaster]
> >gi|17863032|gb|AAL39993.1| SD09634p [Drosophila melanogaster]
> >gi|20043237|dbj|BAA87877.1| Dak2 [Drosophila melanogaster]
> >gi|21626704|gb|AAF47139.2| CG3140-PA [Drosophila melanogaster]
> 
> which is what is expected.  I also tested a very large BLAST XML report I
> generated from NCBI which also works.
> 
> XML::SAX requires a backend parser, usually XML::SAX::ExpatXS or XML::LibXML
> (XML::SAX::Expat will not work).  It comes with XML::SAX::PurePerl by default.  
> 
> What do you get when you use the following statement on the command-line:
> 
> perl -MXML::SAX -e 'print ref(XML::SAX::ParserFactory->parser()),"\n"'
> 
> It should print out the backend parser class (XML::SAX::ExpatXS for me).
> 

Ahhh. Running perl -MXML::SAX -e 'print
ref(XML::SAX::ParserFactory->parser()),"\n"'

returns: 
XML::SAX::PurePerl

I was not aware that I had to install ExpatXS. I will do that and it will
probably fix the problem.  Thanks =)


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