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$i=0;
$line = join '', grep { $i++ % 2 ? {s/,/ /g} : 1} split /"/,$line;

while(<DATA>) {
  print;
  $i = 0;
...
one,"two,three,five",four
"one,two",three
one,two,"three,"

one,two,three
one,two,three

...

one,two,"three,"
one,two,three