my @array;
while(<$file>){
  chomp;
  tr/A-Z//d;
  push @array, [split /\s+/];
}

##</code><code>##

my @array;
while(my $line = <$file>){
  chomp $line;
  $line =~ tr/A-Z//d;
  push @array, [split /\s+/, $line];
}