[Biojava-l] BLASTLikeSAXParser and HMMER

Iris Pallida iris.pallida at free.fr
Wed Feb 4 12:17:51 EST 2004

I'm a (french) newbie...
I would like to use the script from Biojava In Anger ("How do I set up a BLAST 
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 a 
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 framework").
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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