load the data into a temp table as it is.
then
insert into the target table from temp table along with the sequence.no.
-- target table
mag@itloaner1_local > create table jk
  2  (id number,
  3   ename varchar2(14));

Table created.
-- sequence
mag@itloaner1_local > create sequence asf
  2  start with 1
  3  increment by 1;

Sequence created.

- let emp be the temp table which you have loaded.
mag@itloaner1_local > ed
Wrote file afiedt.buf

  1* insert into jk (select asf.nextval,ename from emp)
mag@itloaner1_local > /
mag@itloaner1_local > select * from jk;

        ID ENAME
---------- --------------
         1 SMITH
         2 ALLEN
         3 WARD
         4 JONES
         5 MARTIN
         6 BLAKE
         7 CLARK
         8 SCOTT
         9 KING
        10 TURNER
        11 ADAMS
        12 JAMES
        13 FORD
        14 MILLER
        15 SMITH
        16 ALLEN
        17 WARD
        18 JONES
        19 MARTIN
        20 BLAKE
        21 CLARK
        22 SCOTT
        23 KING
        24 TURNER
        25 ADAMS
        26 JAMES
        27 FORD
        28 MILLER

28 rows created.