#!/usr/bin/perl -w

use strict;
use warnings;
use Bio::SeqIO;
use Bio::Tools::Run::RemoteBlast;
use Bio::Seq;
use IO::String;
use Bio::SearchIO;

my $prog   = 'blastp';
my $db     = 'swissprot';
my $e_val  = '20000';
my $matrix = 'PAM30';

#my $outfile = 'Output';

my @data;
my $line_dataArray;
my $rid;
my $count = 1;

my @params = (
    '-prog'   => $prog,
    '-data'   => $db,
    '-expect' => $e_val,
    '-matrix' => $matrix
);

my $seqio_obj = Bio::SeqIO->new(
    -file   => "Perm.txt",
    -format => "raw",
);

print "entering blast....";
my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
print "Blast entered successfully \n";

while ( my $query = $seqio_obj->next_seq ) {
    print "submit Sequence...just do it....\n";
    my $r = $factory->submit_blast($query);
    print $query->seq;
    print "\n";

    # Wait for the reply and save the output file
    print "entering while loop for saving Output.... \n";
    while ( my @rids = $factory->each_rid ) {
        foreach my $rid (@rids) {
            my $rc = $factory->retrieve_blast($rid);
            if ( !ref($rc) ) {
                print '$rc is not a ref!', "\n";
                if ( $rc < 0 ) {
                    print "Remove rid ...\n";
                    $factory->remove_rid($rid);
                }
                # sleep 5;
            }
            else {

                print "retrieved Results successfully \n";
                print $rid;
                print "\n";
                my $filename = "$count.out";
                $factory->save_output($filename);
                print "File saved successfully \n";
                $count++;
                $factory->remove_rid($rid);
            }
        }
        print "\n";
        print "\n";

    }
}