Hi, As an FYI, people should note that at this time, the -F option of blastall (filter output) for -m 7 option (XML output) does not work, it defaults to -F False. Not a big problem, but I was confused for a bit when my normal output and xml output were giving me different results. The default output with -F false made the results the same.
Thankfully, NCBI confirmed this for me and is looking into it. -Mat -----Original Message----- From: Jason Stajich [mailto:[EMAIL PROTECTED]] Sent: Wednesday, March 06, 2002 10:41 AM To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED] Subject: Re: [Biojava-l] Blast-xml parser We have a soln for this in bioperl, consider this script in bioperl (using the live cvs code or 1.0alpha2-rc this weekend) #!/usr/bin/perl -w use strict; use Bio::SearchIO; use Bio::SearchIO::Writer::HTMLResultWriter; my $in = new Bio::SearchIO(-format => 'blastxml', -file => shift @ARGV); my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); my $out = new Bio::SearchIO(-writer => $writer); $out->write_result($in->next_result); --- run like this % perl htmlwriter.pl file.xml > file.html On Wed, 6 Mar 2002 [EMAIL PROTECTED] wrote: > Hi, there, > I saw your mail, while looking desperately for a possibility to convert blast > output in xml format back to simple text output for simple biologists like me. > Any help at any point from anybody? That would be great! > > Thanks a lot! > > Best wishes > > Edda > > > > > > **************************************************************************** ********* > Wiepert, Mathieu [EMAIL PROTECTED] > Fri, 8 Jun 2001 07:35:26 -0500 > > Previous message: [Biojava-l] blast xml parser > Next message: [Biojava-l] LocationTools + Decoratorated Locations = ? > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > > > > My 2 cents... > > Thank you for pointing out jaxb, that looks like just what I need at the > moment :) > > In regards to your other comments, I ditto Simon on the use of the SAX > framework. Saved me tons of time. When the Biojava SAX components were > first written, I believe there was no XML format for BLAST outputs from any > program. When I was adding a little functionality, XML just came to NCBI as > I was doing it, and GCG didn't have it yet. Now that these things exist, > you may not even need the Biojava SAX parser if you are comfortable with > XSLT. The uses I saw with parsing BLAST was to get interesting bits from a > file to build a datamining tool. I saw my possibilities for dealing with > Blast output as, among other things, > - a content handler in java with Biojava SAX2 compliant parser and text > Blast file > - a content handler in java with SAX2 compliant parser and XML Blast file > - a stylesheet in java with XALAN XSLT processor > - standalone XSLT processor like Saxon against text Blast files with Biojava > SAX parser plugged in > - standalone XSLT processor like Saxon against XML BLAST files. > > This list is not exhaustive, I am sure, and there are different reasons > people might want to use them. One reason to go with plain SAX rather than > XSLT, as Simon has pointed out to me before, is if you have very large blast > files (and I do), using XSLT is not great. It usually tries to instantiate > your whole document in memory. A sax parser is then just the trick. There > are ways around this, but I have not explored them. > > I can certainly see possibilities to take blast output (in either form, text > or XML), and constitute Biojava objects with direct binding, using jaxb, if > that is what it can do. Al the java solutions above could use that quite > nicely. So, who wants to volunteer to look into this? :) > > > -mat > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > -- Jason Stajich Duke University [EMAIL PROTECTED] _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
