[Biojava-l] BLASTLikeSAXParser and HMMER

[mark.schreiber at group.novartis.com]

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
        cc: 
        Subject:        [Biojava-l] BLASTLikeSAXParser and HMMER


Hello,
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 
one...
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

Iris


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