Something like this might do the job for you:

while (<>){
    $entry = SWISS::Entry->fromText($_);
    print "Entry $counter\n";
    foreach my $one_line (split /\n/,$entry) {
      # do something with each line now
    }
}
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This assumes that the Entry->fromText() method is returning the text from the file in one big string that you simply want to break on newlines.

If you're really going to be processing a bunch of text like this, you may also want to run with use strict and use warnings, test your file opens/reads to make sure they worked properly, and otherwise armor-plate your code.