create_test_file.sh

#!/bin/bash

#
# First, create a test file with the three 
# different line ending types LF, CR & CRLF
#

echo -en 'unix!\nclassic mac!\rdos!\r\n' > orig.txt

exit $?

read_file.php

<?php                                                                                                                   

/*
 * Look out for Classic Mac (CR) line endings etc.
 */
ini_set('auto_detect_line_endings', true);

/*
 * Files
 */
$orig = 'orig.txt';
$edit = 'edit.txt';

/*
 * Regex with perl - replace Unix LF with CR
 * using PHP backticks - same as shell_exec()
 * 
 * Write to a clean output file, or add -i for 
 * edit-in-place if you're feeling confident :)
 */
`perl -pe 's/\n/\r/g' $orig > $edit`;

/* 
 * Read normalised file contents into array from file $edit
 * Strip newlines from each element.
 * Skip empty lines, which will occur when we convert a DOS CRLF into a CRCR ;)
 */
$lines = file($edit, FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES);

/*
 * Ta-dah!
 */
var_dump($lines);

result.txt

array(3) {
  [0]=>
  string(5) "unix!"
  [1]=>
  string(12) "classic mac!"
  [2]=>
  string(4) "dos!"
}

Note: useful commands to view non-printing characters:

cat -v orig.txt
od -c orig.txt
file orig.txt