I have a perl script that tries to merge 3 files into one file. However due to some issues with the algorithm it is currently taking a long time to finish. Need some suggestions/advice from the expert monks here. Any help is much appreciated.

Example of Input and Output files

Inputfile1 === Inputfile 2 === Inputfile3

A1 B1 ====== B3, C3, D3 ====== B4
A2 B2 ====== B7, C7, D7 ====== C5
A3 B3 ====== B10, C10, D10 ====== D1
A4 B4 ====== B1, C1, D1 ====== D20
….
….

Output file should look like this

A1 B1 ====== B1 C1 D1 ====== B1 C1 D1
A2 B2 ====== B2 C2 D2 ====== B2 C2 D2
A3 B3 ====== B3 C3 D3 ====== B3 C3 D3
A4 B4 ====== B4 C4 D4 ====== B4 C4 D4
A5 B5 ====== NOT_FNDinFile2 ====== B5 C5 D5
A6 B6 ====== B6 C6 D6 ====== NOT_FNDinFile3
A7 B7 ====== NOT_FNDinFile2 ====== NOT_FNDinFile3
NOT_FNDinFile1 ====== B8 C8 D8 ====== B8 C8 D8
…… ……

Here is my Code..

First I merge File1 and File2 and create a Output file OUT1
Next I merge the Output file 1 and File3.

open(OUT1, '>', $File4)
    or die("Can't create output file \"$File4\": $!\n");
open(OUT2, '>', $File5)
    or die("Can't create output file \"$File5\": $!\n");

%file2_data;
{
   open($fh_keys, '<', $File2) or die("Can't open key file \"$File2\":
+ $!\n");

   while ($line1 = <$fh_keys>) 
   {
       chomp($line1);
       $line1 =~ s/^\s+//; # Remove the space from begining of the lin
+e
       $line1 =~ s/\s+$//; # Remove the space from end of the line
       $first = (split /\t/, $line1)[0];
       $file2_data{$first} = $line1;
   }
}
close($fh_keys);

%file1_data;
{
   open($fh_in, '<', $File1)
      or die("Can't open input file \"$File1\": $!\n");

   while (<$fh_in>) {
       chomp;
       $flag = 0;
       $sec = (split /\t/, $_)[1];
       $file1_data{$sec} = $_;
       if ($file2_data{$sec})
       {
           print OUT1"$_\tFOUND_Data\t$file2_data{$sec}\n";
       }
       else
       {
               print OUT1"$_\tNOTFOUND_IN_FILE2\n";
       }
   }
}
close($fh_in);

while ( ($KEY_1, $VALUE_1) = each %file2_data )
{
    if ($file1_data{$KEY_1})
    {
        print OUT1"$file1_data{$KEY_1}\tFOUND_Data\t$VALUE_1\n";
    }
    else
    {
        print OUT1"$VALUE_1\tNOTFOUND_IN_FILE1\n";
    }
}

open my $File3_IN1, q{<}, "$File3"
    or die qq{Can't open "$File3": $!\n};

my @numbers = ();

while (<$File3_IN1>)
{
    chomp;
    $_ =~ s/^\s+//;
    $_ =~ s/\s+$//;
    if ($_ == "B") {
        push @numbers_B, $_;
    }
    els if ($_ == "C") {
        push @numbers_C, $_;
    }
    els if ($_ == "D") {
        push @numbers_D, $_;
    }
}
close($File3_IN1);
close(OUT1);

my $rxFindB = do{
   local $" = q{|};
   qr{(@numbers_B)};
   };

my $rxFindC = do{
   local $" = q{|};
   qr{(@numbers_C)};
   };

my $rxFindD = do{
   local $" = q{|};
   qr{(@numbers_D)};
   };

open OUT1_IN2,"cat $File4 |" or die "Can't open $File4: $!\n";
while (<OUT1_IN2>)
{
    chomp;
    if m{$rxFindB} {
        print OUT2"$_\t$1\t";
    }
    else {
        print OUT2"$_\tNOT_FOUND_B_InFile3\t";
    }
    if m{$rxFindC} {
        print OUT2"$2\t";
    }
    else {
        print OUT2"$_\tNOT_FOUND_C_InFile3\t";
    }
    if m{$rxFindD} {
        print OUT2"$3\n";
    }
    else {
        print OUT2"$_\tNOT_FOUND_D_InFile3\t";
    }
}
close(OUT1_IN2);
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