Module:Bio::SearchIO::blastxml

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Pdoc documentation: Bio::SearchIO::blastxml	CPAN documentation: Bio::SearchIO::blastxml

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This is a Bio::SearchIO plugin module which parses BLAST XML output. This module requires XML::SAX and one of the following backend parsers:

• XML::SAX::ExpatXS - SAX2-compliant, XS-based based interface to expat
• XML::LibXML - comes with a SAX2-compliant module (XML::LibXML::SAX)
• XML::SAX::PurePerl - if you have installed XML::SAX, you already have this module.

Of the above, XML::SAX::ExpatXS is by far the fastest; the default XML::SAX::PurePerl parser is the slowest.

Note

1. BioPerl currently requires the latest version of XML::SAX (v 0.15). Older versions have a known bug (Issue #2159) in XML::SAX::PurePerl which affects encoded characters; this does not cause XML parsing to fail but leads to other errors.
2. Only the latest version of XML::SAX::Expat (v. 0.38) works; it fixes a bug which required external entity validation (not possible with BLAST XML). It is highly recommended that anyone using this module switch to using XML::SAX::ExpatXS, which is actively maintained.

If you are interested in speed-testing a particular SAX2-based XML::SAX backend, you can do so by the following:

use Bio::SearchIO;
 
$XML::SAX::ParserPackage = 'XML::SAX::PurePerl';
 
my $parser = Bio::SearchIO->new(-verbose => 1,
                                -format => 'blastxml',
                                -file => shift);
 
my $ct = 0;
while (my $res = $parser->next_result) {
    # do whatever here 
}

If ParserDetails.ini doesn't exist, you can use the following to add it (run only if ParserDetails.ini doesn't exist!):

perl -MXML::SAX -e "XML::SAX->add_parser(q(XML::SAX::ExpatXS))->save_parsers()"