Yes it could be nice... For the moment, as I said before the biojava blast parser seem to doesn't work I made my own EBI result parser by using XMLBeans and the XML schema of the EBI XML result.
thanks for your help Bertrand 2007/9/6, Stefan Goetz <[EMAIL PROTECTED] >: > > Hi Bertrand, > Blast2GO uses the NCBI Qblast to run, retrieve and parse blasts since > several years and is completly implemted in Java and works stable. Maybe > you would like to have a look at the aplication first and if you think > that would suit you or be helpfull we can see if I can "cut out" some > code. > Try http://www.blast2go.org/. > Best regards, > Stefan > > > > -----Original Message----- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of > > bertrand beckert > > Sent: Thursday, September 06, 2007 3:21 PM > > To: Mark Schreiber > > Cc: [email protected]; Dickson Guedes > > Subject: Re: [Biojava-l] How to launch a blast on ncbi server > > via biojava? > > > > > > Thanks for all those answers > > > > So first I tried the NCBI blast interface which you can found at: > > http://users.encs.concordia.ca/~f_kohant/ncbiblast/<http://users.encs.concordia.ca/%7Ef_kohant/ncbiblast/> > > which work, but the result are in xhtml format.... > > then I test the EBI webservice for NCBI blast which also work > > and teh result > > are in xml format. > > I use the biojava Blast XML parser, but always some exception occurs: > > org.xml.sax.SAXException : Could not recognise the format of > > this file as one > > supported by the framework > > at org.biojava.bio.program.sax.BlastLikeSAXParser.parse( > > BlastLikeSAXParser.java:182).... > > I also tried to put the parsing in the lazy mode but it doesn't change > > anything. > > > > Remark: > > the BlastLikeSAXParser seem to be able to parse the NCBI > > Blast version: > > 2.0.11 , 2.2.2 , 2.2.3 > > and the blast version received is : program > > name="NCBI-blastn" version=" > > 2.2.15 ".... > > > > Bertrand > > > > > > 2007/9/4, Mark Schreiber <[EMAIL PROTECTED] >: > > > > > > Hi - > > > > > > BioJava doesn't have a mechanism to do this however EBI > > does expose a > > > webservice for NCBI BLAST. The details can be found at > > > http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast > > > > > > They have a java client with source code you could reuse. > > > > > > You can then use biojava to parse the results. If the results are in > > > XML you can use biojava's BLAST XML parser or you could > > just use XPath > > > to get the bits you want. > > > > > > If you build a solution that makes use of biojava it would > > be great if > > > you can add it to the cookbook section of the biojava wiki. > > > > > > - Mark > > > > > > On 9/4/07, bertrand beckert <[EMAIL PROTECTED]> wrote: > > > > Thanks for this code... > > > > but this piece is good if you want to retrieve a specific > > sequence with > > > a > > > > particular ID... > > > > What I want to do, is to submit a blast and then retrieve > > the result and > > > > then parse the result in oder to know what are the ID.... > > > > I already found in the NCBI site ( > > > > http://users.encs.concordia.ca/~f_kohant/ncbiblast/<http://users.encs.concordia.ca/%7Ef_kohant/ncbiblast/>) > a > > java interface > > > but > > > > the documentation is not so nice....and the link with > > biojava is quit > > > > obscure for me.... > > > > > > > > could you help me please > > > > > > > > thanks for all > > > > > > > > Bertrand > > > > > > > > > > > > > > > > > > > > > > > > > > > > 2007/9/4, Dickson Guedes < [EMAIL PROTECTED]>: > > > > > > > > > > Hi Bertrand, > > > > > > > > > > > > > > > You may use a code like this: > > > > > > > > > > > > > > > try { > > > > > NCBISequenceDB impSequence = new NCBISequenceDB(); > > > > > > > > > > Sequence mySequence = > > impSequence.getSequence("156447465"); > > > > > > > > > > System.out.print( > > > > > mySequence.getAnnotation() > > > > > .getProperty("description") > > > > > .toString() > > > > > ); > > > > > } catch (BioException e) { > > > > > System.out.println(e.getMessage()); > > > > > } > > > > > > > > > > > > > > > []s > > > > > Guedes > > > > > > > > > > -----Mensagem original----- > > > > > De: [EMAIL PROTECTED] > > > > > [mailto:[EMAIL PROTECTED] Em nome > > de bertrand > > > beckert > > > > > Enviada em: terça-feira, 4 de setembro de 2007 06:10 > > > > > Para: [email protected] > > > > > Assunto: [Biojava-l] How to launch a blast on ncbi > > server via biojava? > > > > > > > > > > Hi, > > > > > > > > > > Sorry for this silly question, but I would like to know if it is > > > possible > > > > > to > > > > > launch some blast via biojava on the ncbi server for an > > example and > > > also > > > > > to > > > > > retrieve the result as it is possible in in the bioperl project. > > > > > I found some information in the biojava cookbook as > > how to parse some > > > > > blast > > > > > file result but I didn't find any information/example > > for launch blast > > > on > > > > > the ncbi server.... > > > > > Could you help me please > > > > > > > > > > Thanks > > > > > > > > > > Bertrand > > > > > _______________________________________________ > > > > > Biojava-l mailing list - [email protected] > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > > > > > > > -- > > > > > Esta mensagem foi verificada pelo sistema de antivírus e > > > > > acredita-se estar livre de perigo. > > > > > > > > > > Prefeitura Municipal de Florianopolis - PMF > > > > > PMF.SC.GOV.BR > > > > > -- > > > > > > > > > > > > > > > > > > > > > > -- > > > > Bertrand BECKERT > > > > PhD student > > > > IBMC - UPR 9002 du CNRS - ARN > > > > 15, rue Rene Descartes > > > > F-67084 STRASBOURG Cedex > > > > > > > > [EMAIL PROTECTED] > > > > [EMAIL PROTECTED] > > > > > > > > _______________________________________________ > > > > Biojava-l mailing list - [email protected] > > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
