Simply use a loop in Perl:

for my $c (1..24) {
    my $filename = "chr$c";
    open my $IN, '<', $filename or die "Cannot open '$filename' for re
+ading: $!";
    open my $OUT, '<', "$filename.out" or die "Cannot open '$filename.
+out' for writing: $!";
    while (my $line = <$IN>) {
         ...
    }
    close $IN;
    close $OUT;
}
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