[Biojava-l] How to get full query description from blast result

[Simon Foote]

Mark is right
A quick look at the code shows that for the query line, it extracts 
everything upto the first whitespace and puts that into the queryId and 
everything else is discarded.
To get the full description, some additional code is needed to populate 
a queryDescription with everything from the query line upto the query 
length information which is contained in parentheses.

Simon

Bioinformatics Specialist
Institute for Biological Sciences | Institut des sciences biologiques
National Research Council of Canada | Conseil national de recherches Canada
Ottawa, Canada K1A 0R6
Telephone | Téléphone 613-990-3600 / Facsimile | Télécopieur 613-990-9092
Government of Canada | Gouvernement du Canada



Mark Schreiber wrote:
>
> Hi -
>
> If you use the BlastEcho program on the cookbook pages you can find
> out if and how the information is being parsed and where it goes.
>
> It is possible it is not parsed. In this case you could add a feature 
> request.
>
> - Mark
>
> On Thu, Oct 30, 2008 at 10:10 PM, Richard Holland
> <holland at eaglegenomics.com> wrote:
> >
> > Good question!
> >
> > Can someone who knows a lot about the blast parser internals provide
> > David with an answer to his question?
> >
> > cheers,
> > Richard
> >
> > 2008/10/29 David Toomey <dtoomey at rcsi.ie>:
> > > Hi
> > >
> > > I am parsing blast results and I need to get the complete query 
> description line but I can only work out how to get the first part of 
> the line. So for example in the blast result query
> > >
> > > Query= sp|Q8I5D2|ABRA_PLAF7 101 kDa malaria antigen OS=Plasmodium
> > > falciparum (isolate 3D7) GN=ABRA
> > >
> > > I need to get all of the description above but I can only seem to 
> retrieve the first part 'sp|Q8I5D2|ABRA_PLAF7' which I get from the 
> queryId property of the annotation
> > >
> > > Can anyone point me in the right direction for retrieving the 
> complete query description?
> > >
> > > Thanks
> > >
> > > Dave
> > >
> > >
> > > _______________________________________________
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> > >
> >
> >
> >
> > --
> > Richard Holland, BSc MBCS
> > Finance Director, Eagle Genomics Ltd
> > M: +44 7500 438846 | E: holland at eaglegenomics.com
> > http://www.eaglegenomics.com/
> > _______________________________________________
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