[Biojava-l] parse blast results

[Keith James]

>>>>> "Richard" == richard cai <cairi1@yahoo.com> writes:

    Richard> Thanks, Howard.  This is exactly what I need.  Richard
    Richard> Cai


    Richard> --- Howard Ungar <howard_ungar@yahoo.com> wrote:
    >> By "QueryId" do you mean the line in the Blast report that
    >> starts with "Query="?  If so, then I have done exactly what you
    >> are trying to do.

This stems from the fact that the DTD has undergone recent
modifications since Simon's group first commited their code. They
refined the DTD, while incorporating a couple of suggested changes,
one of which was adding QueryId.

This is why the DTD reads, for example:

<!ELEMENT biojava:Header (biojava:RawOutput, QueryId?, DatabaseId? )>

so that the new elements (here QueryId and DatabaseId) are not (yet)
mandatory. This avoids breaking existing code, but leaves extraction
of this information to the user (it's embedded in the
biojava:RawOutput element). See Javadoc in
org.biojava.bio.program.ssbind.BlastDBQueryHandler.

It's on my "to do" list, but time constraints etc.  I'll add any
patches which anyone cares to provide.

cheers,

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK