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 <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
02/05/2004 01:17 AM
To: [EMAIL PROTECTED]
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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