[Biojava-l] Blast SAX parser output

[mark.schreiber at group.novartis.com]

Use a different SearchContentHandler (or Override BlastHitSummaryWriter) 
to write to a file instead of STDOUT. Or you could redirect STDOUT to a 
file (are you allowed to do that with a cron job??)





"Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
Sent by: biojava-l-bounces at portal.open-bio.org
12/30/2004 11:54 AM

 
        To:     <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Blast SAX parser output


Is there any way to stop the blast parser code from outputting progress? I 
get lots of the following and its clogging up my unix mailbox as the job 
is run through cron:

obj=score               317
obj=expectValue         7e-86
obj=numberOfIdentities          158
obj=alignmentSize               160
obj=percentageIdentity          98
obj=numberOfPositives           159
obj=numberOfPositives           159
obj=queryFrame          plus2
obj=querySequenceStart          29
obj=querySequenceEnd            508
obj=querySequence DKHWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKD
EVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKV
TGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMM
obj=subjectSequenceStart                31
obj=subjectSequenceEnd          190
obj=subjectSequence DKEWIPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKD
EVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKV
TGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMM
....

The code producing this is:

            File parsedBlast = safe.tempfile();
            SearchContentHandler handler = new BlastHitSummaryWriter(new 
BufferedWriter(new FileWriter(parsedBlast))); 
            SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
            adapter.setSearchContentHandler(handler);
            BlastLikeSAXParser breader = new BlastLikeSAXParser();
            breader.setModeLazy();
            InputSource is = new InputSource(new FileReader(blast));
            breader.setContentHandler(adapter);
            breader.parse(is);

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199 
 
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