Actually, my DATA file is huge.

For example something like this:

open my $IN1, "<", "1.fa" or die "Cannot open input file";
open my $OUT, ">", "1.txt" or die "Cannot open output file";
while (my $line = <$IN1>) {
    # Do here whatever transformation/substitution you need to $line
    print $OUT $line;
}
close $IN1;
close $OUT;
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