[Bioperl-l] newbie question on blast

[Paul Gordon]

Hi Tania!

You should probably download bioperl 0.7 if you get a chance...
> I am learning to use bioperl 6 and trying to do some local blasts.
> 
> I have a fasta file (test.txt) to blast again a small database called
> ecoli.nt
> 
> below is the code:
> 
> %runParam = (
>     -remote => 'local',
>     -prog => 'blastp', # program name
>     -database =>'ecoli.nt', # database
>     -seqs => 'test.txt'
> );
I think instead of 
     -remote => 'local',
you should say
     -method   => 'local',

Also, you may need to customize the local blast module to fit your
site...
 
> However, even though I say that I want to run the blast locally, I get an
> error saying that
> that IO::Scalar is needed for remote blast. I've pasted  the error below:
Because of the -remote argument it is invoking Webblast, which tells you
that extra modules not required at BioPerl install time are needed to 
use this module (this is so people who are never going to run networked
modules don't need to install superfluous code).

> ================================================== WARNING: COULDN'T LOAD
> THE LWP MODULE.
> 
>    LWP (libwww-perl) is now required to run remote Blasts.
>    Download it from CPAN: http://www.perl.com/CPAN/.
> ==================================================
> 
> 
> ================================================== WARNING: COULDN'T LOAD
> THE IO::Scalar MODULE.
> 
>    IO::Scalar is now required to run remote Blasts.
>    This module is included in the IO-stringy collection
>    from CPAN: http://www.perl.com/CPAN/.
> ==================================================
>                                                           Can't locate
> IO/Scalar.pm in @INC (@INC contains: /usr/local/BioPerl/bioperl-live
> /usr/local/Ensembl/ensembl-0.8.0/software/ensembl/modules )
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>