strInp = OpenRead  ["Test.in"];
strOut = OpenWrite ["Test.out"];

While[(str=Read[strInp, Number) != EndOfFile,

     out = yourprocess[str];

     Write [strOut,out];
];

Close [strOut];
Close [strInp];

(* Now show the output file *)
FilePrint ["Test.out]

(* step one: get data *)
data = Import["ideone_fM0rs.txt", "Lines"];

(* step two: ??? *)
res = {};
Module[{value, result},
  value = #;
  result = yourCodeHere[value];
  AppendTo[res, result];
]& /@ data;

(* step three: PROFIT! *)
Export["out.txt", res, "Lines"];

data = Import["ideone_fM0rs.txt", "Lines"];

res = Reap[Module[{value, result, tag},
  value = #;
  result = yourCodeHere[value];
  tag = generateTag[value]
  Sow[result, tag];
]& /@ data, _, Rule][[2]];

Export["out.txt", res, "Lines"];

data = ReadList["Test.in", Number, RecordLists-> True];

vals = Import["http://ideone.com/fM0rs",
  "Table"] /. {aa_ /; ! NumberQ[aa] && FreeQ[aa, List], ___} :>
  Sequence[] /. {} :> Sequence[]