[Bioperl-l] parsing blast reports

[Chris Fields]

Joan,

Yes; use IO::String, like so:

use IO::String;

my $fh = IO::String->new($report_bls);
my $in = Bio::SearchIO->new(-format => 'blast', 
                            -fh     => $fh);

# the rest as normal

chris

On Wed, 2010-04-07 at 17:23 +0100, Joan Segura Mora wrote:
> Dear bioperl developers,
> 
> I am using bioperl to parse a Blast report. I am using the object
> Bio::SearchIO. In all the examples that I have found the constructor
> method read the report from a file, EX:
> 
> my $in = new Bio::SearchIO(-format => 'blast', 
>                            -file   => 'report.bls'); 
> 
> I would like to know if the constructor can get the blast report from a perl variable ($report_bls)
> 
> thanks a lot,
> Joan
> 
>