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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