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:[EMAIL PROTECTED] > Sent: Thursday, 10 July 2003 10:48 a.m. > To: [EMAIL PROTECTED] > 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 > > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
