def test_window_iterator(config):
seq = "AAAAC"
expected_windows = ["AAA","AAA","AAC"]
expected_windows2 = ["AAA","AAC"]
test1 = ensure_eq( expected_windows,
list(window_iterator(seq, 3)))
test2 = ensure_eq( expected_windows2,
list(window_iterator(seq,3,2)))
return [test1, test2]
def test_get_marked_ranges(config):
test_arr = [0,0,0,1,1,1,0,0,1,0]
expected_ranges = [(3,5),(8,8)]
range_test = ensure_eq(expected_ranges,
get_marked_ranges(test_arr))
return range_test
def test_percent_gc(config):
seq = "AAACCCGGG"
expected_pcts = [float(1)/4,
float(2)/4,
float(3)/4,
float(4)/4,
float(4)/4,
float(4)/4]
return ensure_eq(expected_pcts,
map(percent_gc,
window_iterator(seq,4)))
def test_coverage_array_from_ranges(config):
ranges_ok = [ (1, 3),
(3, 4),
(3, 5) ]
ranges_ok_expect = [0,1,1,3,2,1]
range_test = ensure_eq(ranges_ok_expect,
coverage_array_from_ranges(ranges_ok))
return range_test