Le 24/11/06 18:08, « David Huen » <[EMAIL PROTECTED]> a écrit :
> On Nov 24 2006, Benoit VARVENNE wrote: > >> Hello, >> >> I'm parsing blast results using biojava1.5 and a BlastXMLParserFacade with >> the code put at the end of this mail. >> >> I've tried this with a blastN query and there i got no trouble. >> However, i've tried to do exactly the same thing with a BlastP query and >> i've got the exception cited at the end of this mail. >> >> I've verified and the two infiles (blastn/blastp) seem to have the same >> structures (except that one is for prot so data are different). (Please >> find them as attached if you're used to this). >> >> Can someone help me ? I don't understand why it works in a case and not in >> the other one ... >> > I am uncertain whether BlastXMLFacade will actually support a protein > sequence parse. It was originally developed to handle blastn. Anyone else > tried it with blastp? > > I'm offline till Sunday so I can't reply till then. > > Regards, > David Huen > David, As BlastLikeSAXParser seemed to support older versions of NCBI blastP (see "http://www.biojava.org/wiki/BioJava:Tutorial:Blast-like_Parsing_Cook_Book#S tep_A_-_Create_an_application_that_sets_up_the_parser_and_does_the_parsing") , i'll be surprised if BlastXMLParserFacade does not. However, i'll be very interested if someone's got any information. Can't it be dtd problem ? If yes, can we update dtd sources ? Cheers, Benoît. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
