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

[Schreiber, Mark]

There where a couple of posts on this about two weeks ago, some
solutions where posted to the list, however I think David Huen was going
to post something "official" to BioJava-live on CVS.

See the JavaDoc comments on
org.biojava.bio.program.sax.blastxml.BlastOutputHandler for various
options and a script you could use. Whew that's a long package name :)

- Mark


> -----Original Message-----
> From: DeAngelo Lampkin [mailto:dlampkin at xencor.com] 
> Sent: Thursday, 10 July 2003 10:48 a.m.
> To: biojava-l at biojava.org
> Subject: [Biojava-l] Massaging multi-query BLAST XML output...
> 
> 
> 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
> 
> 
> 
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> 
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