[Bioperl-l] BLASTXML changes (good this time!)

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Thu Feb 8 23:18:33 EST 2007


Chris,

> BLAST XML parsing should now work for any CPAN-based XML::SAX parser!
> XML::SAX::PurePerl (comes with XML::SAX, the slowest)
> XML::SAX::Expat
> XML::SAX::ExpatXS (the fastest)
> XML::LibXML::SAX
> XML::LibXML::SAX::Parser

That's excellent news - thanks for all the work you have put in on
this one. I'm impressed.

This is a good opportunity to encourage people who use Bio::SearchIO
for BLAST parsing to switch to 'blastxml' format over 'blast'.
Although the latter is more human readable, it perenially requires
parser source changes to cope with the variations and new formatting
introduced with each new NCBI BLAST release. Best to use "-m 7" XML
format, and convert as appropriate using one of the
Bio::Search::Writer:: classes.

--Torsten


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