#!/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";
               #my $checkname = "check$count.out";
               $factory->save_output($filename);
               print "File saved successfully \n";
               my $checkinput = $factory->file;
               open(my $fh,"<$checkinput") or die $!;
               while(<$fh>){
                 print;
               }
               close $fh;
               $count++;
               $factory->remove_rid($rid);
           }
       }
       print "\n";
       print "\n";

   }
}