[Bioperl-l] about blast

[Dimitar Kenanov]

Hi guys,
i stumbled upon a problem.

How can i run a psiblast with StandAloneBlastPlus without the query? I 
mean in normal psiblast there is a possibility that one can actually 
blast with the option '-in_pssm' instead of query. Of course first you 
need to run a psiblast with more than one iterations with option 
'-out_pssm' which produces the file which can be used by '-in_pssm'.

Now in BioPerl i removed my query from the options and i got:
----------
MSG: Blast run: query data required, use -query
STACK: Error::throw
STACK: Bio::Root::Root::throw 
/usr/lib64/perl5/site_perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::Tools::Run::StandAloneBlastPlus::run 
/usr/lib64/perl5/site_perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm:216
----------

Somehow it would be nice to check the method args in the module and when 
there is the option '-in_pssm' the check for query should be 
different(opposite to the one now).

I hope i made it clear :)

Cheers
Dimitar

-- 
Dimitar Kenanov
Postdoctoral research fellow
Protein Sequence Analysis Group
Bioinformatics Institute
A*STAR, Singapore
tel: +65 6478 8514