#!/usr/bin/perl -w


use Bio::SeqIO;
use Bio::Tools::Run::StandAloneBlast;
#use Bio::SearchIO::blast;

my $query1_in  = Bio::SeqIO->newFh ( -file   => "roa1.fasta",
				    -format => 'fasta' );
my $query1 = <$query1_in>; 
my $query2_in  = Bio::SeqIO->newFh ( -file   => "roa2.fasta",
				    -format => 'fasta' );
my $query2 = <$query2_in>; 

$factory = Bio::Tools::Run::StandAloneBlast->new('program'  => 'blastp');
$report = $factory->bl2seq($query1, $query2);
print "ref: ", ref($blast_report), "\n";

while(my $hsp = $report->next_feature) {  
  print "homology seq :\n",  $hsp->homologySeq, "\n";
  print "sbjctSeq :\n",  $hsp->sbjctSeq, "\n";}