gistfile1.py

from glob import glob
from astropy import table
import h5py as hdf
from os.path import exists

files = glob('*.fit')

for f in files[:2]:
    print f, '.....',
    if not exists(f.replace('fit', 'hdf5')):
        t =table.Table.read(f, 'r')
        t.write(f.replace('.fit', '.hdf5'),
                path=f.split('_')[1]+'_'+f.split('.')[1])
        print 'done'
    else:
        print 'already done'