[Biojava-dev] problem with blast parser

[Richard Holland]

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Hello.

This is related to your previous email about it not being able to read
all data (e.g. query length).

I believe Andreas Prlic (copied on this) is looking into this, and some
other people might be as well. One of them will get back to you.

cheers,
Richard

Michael Gang wrote:
> Hi All,
> I've observed the following pronlem with the blast parser.
> When parsing a blast with more than one query, it skips a part of the queries.
> When I wanted to understand what the problem is I got to the following
> conclusion.(There are good chances that I am wrong)
> When the BlastSaxParser in the function hitsSectionReached calls the
> line: oHits.parse(oContents,poLine,"Database:");.
> It just get's back when it get to the line :Database= but this is in
> the middle of the next query (the query began with the line "BLASTX
> 2.2.16 [Mar-25-2007]".
> I also tested it with the blastecho program
> Did someone observed the same problem.
>  Can someone help me in this issue ?
> 
> Thanks in Advance,
> Michael
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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