Read Blast Output Directly From Stdout With Bioperl

Hi there,

I finally decided myself to try Perl for a project and I got a question concerning BioPerl. I would like to read the result (blastxml) of a blast query directly from STDOUT. Is it possible ?

Here is my attempt:

   my $command = "echo '>$SeqName\n$_[0]' | blastall -a 4 -p blastn -d $db  $options";

   open $fh,"$command |" || die("cannot run fasta cmd of $command: $!\n");

   my $seqout = Bio::SeqIO->new(-fh => $fh,  -format => 'blastxml');

Also, I manage to catch STDOUT using IO::CaptureOutput, but I cant feed it into Bio::SeqIO. Maybe there is something than can be done with that.

Any help will be appreciated. Thanks