#!/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);
             print "retrieved Results successfully \n";
      if( !ref($rc) ) {
           if( $rc < 0 ) {
               $factory->remove_rid($rid);
           }
           sleep 5;
      } else {
          #my $result = $rc->next_result;
          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";

 
     }
}