The modules mentioned in other responses here will provide you with a robust solution. But if the problem itself interests you, here's a way to approach the task using a lot less code. (I have omitted the hyphenation bit since I don't quite follow your standards for that part).

This approach creates a closure (roughly stated: a state-preserving anonymous subroutine) which you then call to spit out a word at a time for handling. This allows your main loop to focus on building the new lines and to ignore the details of parsing the input and knowing when to read in another line. 

#!/usr/bin/perl -w
use strict;

sub make_word_dispensor {
   my $infile = shift;
   open INFILE, "<$infile" 
      or die "Can't open $infile: $!\n";
   my @words = ();
   return sub {
      unless (@words or (@words = split /\s/, <INFILE>)) {
         close INFILE;
         return undef;
      }
      return shift @words;
   }
}

my $word_dispensor = make_word_dispensor("test.txt");
my $line_length = 50;
my $line = '';
while (my $word = &$word_dispensor()) {
   if (length("$line $word") > $line_length) {
      print "$line\n";
      $line = $word;
   }
   else {
      $line .= ($line ? ' ' : '') . $word;
   }
}
print "$line\n";

[download]

Season to taste. HTH

In reply to Re: Alignment Program by dvergin
in thread Alignment Program by Anonymous Monk

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