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while (<FILE2>) {
  push @col, $_ =~ m/^(\S+)/  unless ...;
}

while(<COL>) {
  $_ =~ s/^(\S)/$1 $col[$i++]/;
  print OUT2 $_;
}

while (<COUNT>){
  ($i, $j) = ...

my ($i, $j)

open (FILE, "test.pat") or die "Can't open test.pat: $!";
open (OUT, ">TRUE_OUTPUTS") or die "Can't open TRUE_OUTPUTS: $!";
...
}
close (FILE);
close (OUT);