#!/usr/bin/perl -w

use Bio::SearchIO;
use strict;

print "start program\n";
my $directory = '/home/Hubert/result_1';
opendir(DIR, $directory) || die("Cannot open directory");
print "opened directory\n";

foreach my $file (readdir(DIR))  {
  if ($file =~ /txt/)   {
    print "read file $file \n";

    $file = $directory . '/' . $file;

    my $search = new Bio::SearchIO (-format => 'blast',
                          
             -file => $file);
               
               
  
    my $cutoff_len = 10;
               
               
  
    #iterate over each query sequence
    print "try to enter while loop\n";
    while (my $result = $search->next_result) {
    print "entered 1st while loop\n";
    
      #iterate over each hit on the query sequence
      while (my $hit = $result->next_hit) {
      print "entered 2nd while loop\n";
        
        #iterate over each HSP in the hit
        while (my $hsp = $hit->next_hsp) {
        print "entered 3rd while loop\n";
            
          if ($hsp->length('sbjct') <= $cutoff_len) {
          #print $hsp->hit_string, "\n";
               
 
            for ($hsp->hit_string) {        #$hsp->hit_string
            print $hsp->hit_string,"\n";

               if (tr/K// >= 2 || tr/R// >= 2 && tr/W// >= 2 ||
                   tr/K// == 1 && tr/R// == 1 && tr/W// >= 2) {
              
              
                           
                print "create and open to write file\n";
                   open (bigShot, ">>result_adv_4.txt") || die ("Could not open file. $!");
                    #print $result->query_name, "\t";
            
#                print $hit->significance, "\t";
                 print bigShot $hit->name, "-->";
                 print bigShot $hit->description, "\n";
                 #print bigShot "Query:   ", $hsp->start('query'), "  ", $hsp->query_string, "  ", $hsp->end('query'), "\n";
                 print bigShot "Seq:     ", $hsp->start('hit'), "  ", $hsp->hit_string, "  ", $hsp->end('hit'), "\n";
                           
#                print $hsp->rank, "\t";
#                print $hsp->percent_identity, "\t";
#                print $hsp->evalue, "\t";
#                print $hsp->hsp_length, "\n";
               
     
                close (bigShot);
               
         
              }#end if condition
            }#end for loop
          }#end if condition
        }#end 3rd while loop
      }#end 2nd while loop
    }#end 1st while loop
  }#end if condition
}#end foreach loop

closedir(DIR);

              if (tr/K/K/ >= 2 || tr/R/R/ >= 2 && tr/W/W/ >= 2 ||
                  tr/K/K/ == 1 && tr/R/R/ == 1 && tr/W/W/ >= 2) {

if ($hsp->hit_string =~ tr/K// >= 2 || $hsp->hit_string =~ tr/R// >= 2 && $hsp->hit_string =~ tr/W// >= 2 ||
                  $hsp->hit_string =~ tr/K// == 1 && $hsp->hit_string =~ tr/R// == 1 && $hsp->hit_string =~ tr/W// >= 2) {