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
---------------------------------------------
This email is confidential and may be privileged. If you are not the intended
recipient, please delete it and notify us immediately. Please do not copy or
use it for any purpose, or disclose its content to any other person. Thank you.
---------------------------------------------
_______________________________________________
Biojava-l mailing list - [email protected]
http://biojava.org/mailman/listinfo/biojava-l
