Hi Rickman1!
In general a great Monk question has some data and actual code that the Monks can run. If you have private data that cannot be disclosed publically, then "dummy up" something that is an acurate representation of the actual data, but is "fake". Use made up names and account numbers, "Luke Skywalker" or whatever.

This code has some issues that I see:

while (my $line = <$fh>) {
    my $val = substr($line, $char_at, $num_chars);
    if ($val eq 'H' or $val eq 'T') {
        my $output = $line;
    }else {    
        chomp $line;
        next unless $line && length($line) >= $char_at;
        push @trnAccounts, substr($line, $char_at, $num_chars);
    }
}
[download]

First, my $output = $line; will never be executed. And even if it is, it will do absolutely nothing. You cannot declare a "my" variable conditionally and use it elsewhere. Use it immediately or not at all. So this whole "if" clause is "nonsense".

Will the condition if ($val eq 'H' or $val eq 'T') ever be satisfied? I think not. $val looks like it is a string of 50 characters, starting at $char_at. This will never equal a single character comparison. Some regex might work, but single character, I think not. You have not chomped the line endings, and this line ending in $val will prevent the "match".

In the "else" clause, the appears to be confusion. next unless $line, will always work! Right up front, while (my $line = <$fh>) says that $line is true otherwise the loop doesn't proceed. push @trnAccounts, substr($line, $char_at, $num_chars);. Well that substr is just $val.

I suggest that you have another "go" at this. Generate say 10 example lines, show your code to process those lines and how it fails. Keep simplifying the example until you cannot reproduce the problem any more. Make it as simple as possible. This process may help you discover your own problem.