Arggh!!!!I didn't find what I wanted!! I used the program you gave me but with a light modification because it didn't recognize my XML file... The parser is, now, a BlastXMLParserFacade.... And it gave me everythings it found in the file..... BUT not what I want!!GRRR...>:( >:( >:(
There is a mark out (I don't know if it's the good word...) in my XML file which frame what I'm searching for : <Hsp_midline>.... Why the parser doesn't see it..?? I didn't really understand how the XML parser works....So, how can I modifie it to find my happiness...?? PLEASE DOC'!!! ;);) Help me!! Thanks for everythings.. Sebastien --- [EMAIL PROTECTED] a écrit : > Hi - > > Try running this program > http://www.biojava.org/docs/bj_in_anger/blastecho.htm > > If you see what you need in the output then it is being read by the > Blast > parser and emitted as an event (which you could listen for). If it > isn't > then the Blast parser is not emitting those events although someone > confident with the blast format could probably modify it so it does. > > In short, it is possible but it might not be implemented ; ) > > - Mark > > > > > > Sébastien PETIT <[EMAIL PROTECTED]> > Sent by: [EMAIL PROTECTED] > 06/28/2005 05:11 PM > > > To: biojava-l@biojava.org > cc: (bcc: Mark Schreiber/GP/Novartis) > Subject: RE: [Biojava-l] BLAST Parser for extracting > all BLAST data? > > > Hi, everybody... > > I'm like Georges....I want to extract data from BLAST files..... > I can have the alignements, no problem...But, now, I want the > alignment > between the 2 sequences (the lines with "+", "-" and some letters in > George's example....) because with this, we can see in a glance if > the > alignment between the 2 sequences is really good or not. > > Is it possible, Docs?? > > Thank you. > > Sebastien > > --- Richard HOLLAND <[EMAIL PROTECTED]> a écrit : > > > BioJava's BLAST framework parses files and fires events for every > > piece of information it finds. The SeqSimilarityAdapter class is an > > example of how to catch these events and construct basic BLAST > result > > objects (SimpleSeqSimilarityHit), however they are not > comprehensive > > and do not record full details of every hit. > > > > If you want the kind of detail you mention below you will have to > > write your own content handler for BLAST parsing and parse it to > the > > BLASTLikeSAXParser when parsing a file. This event handler should > > implement the ContentHandler interface. Look at the source of > > SeqSimilarityAdapter for guidance. You will then receive events for > > every part of the file, from which you can construct your own > custom > > BLAST result objects to describe them. > > > > If you're not sure what tag names to listen for in your > > ContentHandler the easiest thing to do is just run it once and dump > > them all out to see what you get. > > > > cheers, > > Richard > > > > > > -----Original Message----- > > From: [EMAIL PROTECTED] on behalf of Y > D > Sun > > Sent: Sun 6/26/2005 5:42 PM > > To: biojava-l@biojava.org > > Cc: > > Subject: [Biojava-l] BLAST Parser for extracting all > BLAST > data? > > > > Hi, > > > > I want to extract all data from BLASTP results. In the following > hit, > > for example, I need to get the lengths of query and subject > proteins, > > the identities (including all data 54, 124 and 43%), the positives > > (all > > data 79, 124 and 63%), and the gaps (3, 124 and 2%). Can the > > BLASTLikeSAXParser filter all these information? I can't find the > > methods in SeqSimilaritySearchHit and SeqSimilaritySearchSubHit > APIs > > to > > retrieve these data. Does Biojava provide any methods for this > > purpose? > > > > Thanks, > > > > George > > > > > > BLASTP 2.2.5 [Nov-16-2002] > > > > Query= Prot0001 > > (138 letters) > > > > Database: /work/nys1/fasta/protein/AE000782.pro.fasta > > 2407 sequences; 662,866 total letters > > > > Searching.....done > > > > > > Score > > E > > Sequences producing significant alignments: > > (bits) > > Value > > > > Prot0002 > > 100 > > 1e-23 > > Prot0003 > > 74 > > 2e-15 > > Prot0004 > > 43 > > 3e-06 > > > > >Prot0002 > > Length = 138 > > > > Score = 100 bits (250), Expect = 1e-23 > > Identities = 54/124 (43%), Positives = 79/124 (63%), Gaps = 3/124 > > (2%) > > > > Query: 18 > > NARTKFTDIAKTLNLTEAAIRKRIKKLEENQIIKRYSIDIDYKKLGYNMAIIGLDIDMDY > > 77 > > NAR T IAK LN+TEAA+RKRI LE + I Y I+YKK+G + ++ > G+D+D > > D > > Sbjct: 15 > > NARIPKTRIAKELNVTEAAVRKRIANLERREEILGYKAIINYKKVGLSASLTGVDVDPDK > > 74 > > > > Query: 78 > > FPKIIKELEKRKEFLHIYSSAGDHDIMVIAIYK---DLEEIYNYLKNLKGVKRVCPAIII > > 134 > > K+++EL+ + ++ + GDH IM I K +L EI+ + > > ++GVKRVCP+II > > Sbjct: 75 > > LWKVVEELKDLESVKSLWLTTGDHTIMAEIIAKSVQELSEIHQKIAEMEGVKRVCPSIIT > > 134 > > > > Query: 135 DQIK 138 > > D +K > > Sbjct: 135 DIVK 138 > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > > > > > > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > > > > > > > > > ___________________________________________________________________________ > > > Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! > Messenger > > Téléchargez cette version sur http://fr.messenger.yahoo.com > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > > > > ___________________________________________________________________________ Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! 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