[Biojava-l] BLASTLikeSAXParser and HMMER

mark.schreiber at group.novartis.com mark.schreiber at group.novartis.com
Wed Feb 4 21:01:28 EST 2004

Hi -

You may need to call the setModeLazy() method on the BLASTLikeSAXParser 
which will tell it to not care so much about the version number and try 
parsing the file anyway. If you do this you should check the output 
carefully to make sure it hasn't made any mistakes.

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
1 Science Park Road
#04-14 The Capricorn
Singapore 117528

phone +65 6722 2973
fax  +65 6722 2910

Iris Pallida <iris.pallida at free.fr>
Sent by: biojava-l-bounces at portal.open-bio.org
02/05/2004 01:17 AM

        To:     biojava-l at biojava.org
        Subject:        [Biojava-l] BLASTLikeSAXParser and HMMER

I'm a (french) newbie...
I would like to use the script from Biojava In Anger ("How do I set up a 
parser?") in order to parse my file "resut" from hmmpfam.
The API says it is OK for the 2.1.1 version of HMMER and I have the last 
But I've built my result with the hmmer --compat option, in order to have 
2.1.1 compatible file.
The parser doesn't work anyway ("org.xml.sax.SAXException: Program hmmer 
Version 2.3.2 is not supported by the biojava blast-like parsing 
I d'ont know if the hmmer option '--compat' doesn't work or if there is 
another way to do that.
Is there someone here who did it and could help me ?
Thank you in advance


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