[Biojava-l] Massaging multi-query BLAST XML output...

[DeAngelo Lampkin]

Hi guys,

First of all, thanks to Keith and Matthew on the assist with the last question.  And to the rest, shame on you all for not helping sooner! :)

So now for my newest question concerning parsing Blast XML files; specifically the mangled XML file that come out as a result of a multiple query FASTA file search .   I read the JavaDoc on BlastXMLParser and it made reference to a shell script (blast_aggregate) that massages the XML output into something that is, you know, *legal* XML. Is this an actual script floating around somewhere or was it something put in for illustrative purposes only?  I could do it myself, I suppose, but while I like wheels as much as the next guy, I try to avoid reinventing them when possible.  

Thanks again,
DeAngelo Lampkin