$file = fopen("PADNAARFILENU/filename.ext","r");
$contents = fgets($file);
$eachBlock = explode('\n\n\n',$contents); //Of Gebruik 3x PHP_EOL (Geeft einde van een lijn aan)
$newContents = "";
foreach($eachBlock AS $value)
{
  $each = explode('\n',$value) //Of gebruik 1x PHP_EOL
  foreach($each AS $key => $val)
  {
    $newContents .= $value;
    if($key != end($each)) $newContents .=",";
  }
  $newContents .= "\n";
}
$ourNewFileName ="PADVOORDENIEUWEVERSIE/newfilename.ext";
$ourNewFileHandle = fopen($ourNewFileName, 'w') or die("Kan bestand niet aanmaken.");
$stringData = $newContents;
fwrite($ourNewFileHandle, $stringData);
fclose($ourNewFileHandle);

$file = fopen("PADNAARFILENU/filename.ext","r");
$contents = fgets($file);
$eachBlock = explode("\n\n\n",$contents);
$newContents = "";
foreach($eachBlock AS $value)
{
  $each = explode("\n",$value)
  foreach($each AS $key => $val)
  {
    $newContents .= $value;
    if($key != end($each)) $newContents .=",";
  }
  $newContents .= "\n";
}
$ourNewFileName ="PADVOORDENIEUWEVERSIE/newfilename.ext";
$ourNewFileHandle = fopen($ourNewFileName, 'w') or die("Kan bestand niet aanmaken.");
$stringData = $newContents;
fwrite($ourNewFileHandle, $stringData);
fclose($ourNewFileHandle);

<?php
$in  = 'in.txt'; // input file
$out = 'out.txt'; // output file
$cols = array('col1', 'col2', 'col3', 'col4', 'col5'); // names of columns


// open input file for reading
if (($fpIn = @fopen($in, 'r')) === false) {
    die('[error] could not read file '.$in);
}


// open output for writing (will truncate file) and add column header
if (($fpOut = @fopen($out, 'w')) === false) {
    die('[error] could not open '.$out.' for writing');
}
fputcsv($fpOut, $cols);


$data = array(); // temp var for collecting data


// loop through all lines of input file
while (($line = fgets($fpIn)) !== false) {
    if (trim($line) === '') {
        // do nothing
    } else {
        $data[] = trim($line); // trim because might still have newline attached which might break CSV
        // did we collect enough info for one record?
        if (count($data) == count($cols)) {
            // write data to CSV
            fputcsv($fpOut, $data);
            // clear data
            $data = array();
        }
    }
}


// extra check - did we read everything?
if (feof($fpIn) === false) {
    echo '[error] did not reach end of file :(';
}
fclose($fpOut);
fclose($fpIn);
?>[done]