Uh yes,
open the file for reading, and a temp file for writing. Read one line from the file, replace the '"' with whatever you want, and write it to the other file. When done, close both files and move the new over the old one.
I.e. (quick, don't trust this code)
$inFP = fopen("infile.txt", "r");
$outFP = fopen("outfile.txt", "w");
while ($oneLine = fgets($inFP, 4096)) {
$newLine = str_replace('"', 'whatever', $oneLine);
fputs($outFP, $newLine);
}
fclose($inFP);
fclose($outFP);
rename("outfile.txt", "infile.txt");