Hi, you could have a number of next statements to discard records that are not good. For example:

while (<$IN_FILE>) {
     chomp;
     next if /[^ACTG]/; # removes lines with other letters
     next if length != 19; # removes lines not 19 char long
     # I just made up the next rule for the example
     next if /(.)\1\1/; # removes lines where the same letter comes th
+ree times in a row
     # etc.
     # now start doing the real processing
     # ...
}
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The next statement goes directly to the next iteration of the while loop, so that faulty lines are effectively discarded early in the process.