Assuming that the characters on the left of the ">" are unique (or the doubles to the right are unique), the easiest way I can think of to do this is to use a HashMap object. Just split the string on the ">", and use one of them as the key and one as the value. When you're done, just retrieve the 2 collections with the keySet() and values() methods and then convert them with toArray().
I'd also take a look at the string split() method - makes parsing really easy with a fixed format like this.
Edit:
HashMap<String, Double> lists = new HashMap<String, Double>();
while (scanner.hasNext())
{
String[] temp = scanner.next().split(">");
lists.put(temp[0], Double.parseDouble(temp[1]));
}