Shell Programming and Scripting

#! usr/bin/perl
use warnings;
open RAW, "$ARGV[1]";
open ADAPTER, "$ARGV[0]";
@reads =();
@ada =();
while (<RAW>) {
      if (($. -2) % 4 == 0) {push (@reads, $_);             
                            }
              }
while (<ADAPTER>) {                                                    @adapter = split (//);
            $i= -1;
        while (++$i < $#adapter-8) {
                            $_ = "$adapter[$i]$adapter[$i+1]$adapter[$i+2]$adapter[$i+3]$adapter[$i+4]$adapter[$i+5]$adapter[$i+6]$adapter[$i+7]$adapter[$i+8]";
                             push (@ada, $_);                             
                                   }
                  }
@reads1 = ();
foreach $reads(@reads) {                              
             foreach $ada(@ada) {
                                  $reads =~ s/$ada.*|(A{9}|G{9}|C{9}|T{9})[A-Z]+//g; 
                                }                 
                       push (@reads1, $reads);  
                       }
%duplicates = ();
chomp (@reads1);
$i = 0;
open Fasta_reads, ">/home/Desktop/fasta_reads";
foreach (@reads1) { 
            if (length $_ >14) {                                      
                     $duplicates{$_}++;
                  }            }
foreach $count (keys %duplicates) {$i +=1;
               $read_length = length $count;
               $_ = "> $i $read_length $duplicates{$count}\n$count\n";
               print Fasta_reads;
                                  } close Fasta_reads;