PHP- Compare two CSV files, look for duplicates and remove matching rows from one of the files

Here is a script that will loop through both files and output a 3rd file where email addresses in file2 are found in file1.

if (($file3 = fopen("file3.csv", "w")) !== FALSE) {
  if (($file1 = fopen("file1.csv", "r")) !== FALSE) {
    while (($file1Row = fgetcsv($file1)) !== FALSE) {
      if (($file2 = fopen("file2.csv", "r")) !== FALSE) {
        while (($file2Row = fgetcsv($file2)) !== FALSE) {
          if ( strtolower(trim($file2Row[0])) == strtolower(trim($file1Row[1])) )
            fputcsv($file3, $file1Row);             
        }
        fclose($file2);
      }
    }
    fclose($file1);
  }
  fclose($file3);
}

Couple of notes:

• You may need to provide some additional arguments to fgetcsv, depending on how your csv is structured (e.g. delimiter, quotes)
• Based on how you listed the contents of each file, this code reads the 2nd column of file1, and the 1st column of file2. If that's not really how they are positioned, you will need to change the number in the bracket for $file1Row[1] and $file2Row[0]. Column # starts at 0.
• Script is current set to overwrite if file3.csv exists. If you want it to append instead of overwrite, change the 2nd argument of the $file3 fopen to "a" instead of "w"

Example:

file1.csv:

john,[email protected],blah
mary,[email protected],something
jane,[email protected],blarg
bob,[email protected],asdfsfd

file2.csv

[email protected]
[email protected]

file3.csv (generated)

mary,[email protected],something
bob,[email protected],asdfsfd

Solved! The problem was with Mac line breaks. Look at the code below to see the additions at the beginning and end of the code to fix that problem. Thank you Crayon Violent for all of your help!

ini_set('auto_detect_line_endings',TRUE);
if (($file3 = fopen("output.csv", "w")) !== FALSE) {
  if (($file1 = fopen("dirty.csv", "r")) !== FALSE) {
    while (($file1Row = fgetcsv($file1)) !== FALSE) {
      if (($file2 = fopen("clean.csv", "r")) !== FALSE) {
        while (($file2Row = fgetcsv($file2)) !== FALSE) {
          if ( strtolower(trim($file2Row[0])) == strtolower(trim($file1Row[1])) )
            fputcsv($file3, $file1Row);             
        }
        fclose($file2);
      }
    }
    fclose($file1);
  }
  fclose($file3);
}
ini_set('auto_detect_line_endings',FALSE);