Perhaps you could show us the code that you have at present and a very small sample of data that demonstrates the problem. The code below may be a good starting point (you'll have to fill in bits though):

use strict;
use warnings;

my $data = <<DATA;
this is a good \
nice day but not a good nice \
night
DATA

open my $IN, '<', \$data;

...

while (<$IN>) {
    ...
}

close $IN;
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with the intent being that you fill in the ... bits to match your current code with the code above providing a nice framework for the sample.