It looks like the new BLAST+ binary is using a default frame of 0 instead of the old default of 1 for blastp. Hence the illegal frame number (0) error.
Josh Pierre-Yves wrote: > Dear list, > > I am trying to find my way around parsing ncbi blast xml. > I am using a small library which performs the blast online [1] and > returns a FileReader of the xml. > I can convert the FileReader to a string and print it, it seems fine. > (I used the default input shown on [1]). > > So I am now trying to parse it automatically. I looked at [2] and [3] > but I could not get them working. I then found this message from this > mailing list [4] and thus went to use BlastXMLParserFacade. > It returns me an "org.xml.sax.SAXException: illegal frame number > encountered. (0)". > > So my question is then: which method should I use ? > > Thanks in advance, > > Best regards, > > Pierre > > > > [1] http://users.encs.concordia.ca/~f_kohant/ncbiblast/ > [2] http://biojava.org/wiki/BioJava:CookBook:Blast:Echo > [3] > http://biojava.org/wiki/BioJava:Tutorial:Blast-like_Parsing_Cook_Book > [4] http://osdir.com/ml/java.bio.general/2005-06/msg00018.html > > > > _______________________________________________ > 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
