def select_pileup_range_and_truncate_output(
self, pileup, startpos, endpos, pileup_select_range_expected_out,
pileup_truncate_expected_out):
"""
select_pileup_range_and_truncate_output - Checks if the program works
as expected when truncating contiguous start and end regions after
first selecting a specified range.
INPUT:
[2D ARRAY of DICTIONARIES] [pileup]
[INT] [startpos]
[INT] [endpos]
[2D ARRAY OF DICTIONARIES] [pileup_select_range_expected_out]
[2D ARRAY OF DICTIONARIES] [pileup_truncate_expected_out]
RETURN:
TODO
POST:
TODO
"""
pileups = Pileup_List([Pileup(bam) for bam in pileup])
pileups.select_pileup_range(startpos, endpos)
select_pileup = pileups.get_pileups_as_array()
# assert that the pileup positions before startpos and after endpos
# have been ignored
assert select_pileup == pileup_select_range_expected_out
pileups.truncate_output()
truncated_pileup = pileups.get_pileups_as_array()
# assert that the pileup is truncated now as expected
assert truncated_pileup == pileup_truncate_expected_out
def test_truncate_output(self, pileup, expected_truncated_pileup,
expected_left_pos_truncated,
expected_right_pos_truncated):
"""
test_truncate_output - Checks that the expected truncated outputs
matches the actual output.
INPUT:
[2D ARRAY OF DICTIONARIES] [pileup] # to be truncated
[2D ARRAY OF DICTIONARIES] [expected_truncated_pileup]
[2D ARRAY OF DICTIONARIES] [expected_left_pos_truncated]
# number of contiguous left positions that were truncated
[2D ARRAY OF DICTIONARIES] [expected_right_pos_truncated]
# number of contiguous right positions that were truncated
RETURN:
[None]
POST:
Checks that the expected outputs match the actual output
"""
pileups = Pileup_List([Pileup(bam) for bam in pileup])
pileups.truncate_output()
truncated = pileups.get_pileups_as_array()
assert truncated == expected_truncated_pileup
assert pileups.get_num_left_positions_truncated(
) == expected_left_pos_truncated
assert pileups.get_num_right_positions_truncated(
) == expected_right_pos_truncated