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

[David Toomey]

Hi Mark

I tried that and it appears that it is not being parsed. Only the portion of the line up to the first space is returned as queryId. The rest of the line is not returned.
Could this be added to the blast parser?

Cheers

Dave


-----Original Message-----
From: Mark Schreiber [mailto:markjschreiber at gmail.com]
Sent: 31 October 2008 08:01
To: holland at eaglegenomics.com
Cc: David Toomey; biojava-l at biojava.org
Subject: Re: [Biojava-l] How to get full query description from blast result

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
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> --
> 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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