[Biojava-l] NCBI xml parser

[jitesh dundas]

Dear Sir,

I am not using any of those methods. However, I have written a code to parse
through an XML file for pubmed data.

Hope this might help you.

Regards,
Jitesh Dundas

On Mon, Nov 2, 2009 at 7:33 PM, Pierre-Yves <pingou at pingoured.fr> 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/<http://users.encs.concordia.ca/%7Ef_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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> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
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