Hey I have a script below, which takes two files, loops over the lines in the files, and if two certain variables match, combines the files into an output file. It works fine, except I am starting to loop over very large files, and this loop is now taking days instead of minutes. Is there a way to make this more efficient?

#!/us
/bin/perl
use File::Basename;
open (DATA, "file1.out") or die "$!";
while (my $line = <DATA>){
if ($line =~ /(\S+)(\s+)run(\d+)_sub(\d+)_event(\d+)(\s+)(\S+)(\s+)(\S+)(\s+)(\S+)(\s+)(\S+)(\s+)(\S+)(\s+)(\S+)(\s+)(\S+)(\s*)/){
open (REFILE, ">>output.out");
my $var1 = $5;
my $var2 = $9;
my $var3 = $11;
my $var4 = $13;
my $var5 = $15;
my $var6 = $17;
my $var7 = $19;
my $var8 = $7;
my $var9 = $1;
open (DATA2, "file2.out") or die "Cannot open file2";
while (my $line2 = <DATA2>){
if($line2 =~ /(\S+)(\s+)(\S+)(\s+)run(\d+)_sub(\d+)_event(\d+)(\s*)/){
my $var10 = $3;
my $var11 = $7;
if ($var3 == $var10){
if ($var4 == $var11){
print REFILE "$var1 $var2 $var11\n";
} } } }
close(DATA2);
} } close(REFILE); close(DATA);

Original content restored by GrandFather

In reply to quicker way to merge files? by nessundorma

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