[Biojava-l] NCBI xml parser

[Josh Goodman]

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
> 
> 
> 
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