[Bioperl-l] standalone blast on 2 databases

[Benoit Piegu]

Damien Mattei wrote:

>
> I want to do a standalone blast on 2 databases,
> i know it is possible, as i can do it on the
> command line specifying the name of databse with -d "nt htg" option
>  for example,but when i do it in bio-perl i get an error:
>
> @params = ('program'  => 'blastn',
>             'database' => 'nt htg',

try :
'database' => '"nt htg"',

>
>         'outputfile' => 'blast_gmap.out' );
>
>  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>
> result in:
> [blastall] ERROR: Arguments must start with '-' (the offending 
> argument #5 was: 'htg')
> ------------- EXCEPTION  -------------
> MSG: blastall call crashed: 256 /home/dmattei/ncbi/build/blastall -p 
> blastn  -d  /home/dmattei/ncbi/db/nt htg  -i 
> /home/dmattei/tmp/gi5622463  -o  blast1.out
>
> is there a way to blast in both databases?
>
> --------------------------------------
> Damien Mattei



Benoit Piegu
Laboratoire Génome et Développement des Plantes
UMR 5096 - CNRS/UP
52, Avenue de Villeneuve
66860 Perpignan