def __init__(self):
self.hub = Hub()
elem_path = ":memory:"
bam_path = "tests/data/align.bam"
self.hub.connect(CoverageAdapter(bam_path), ElementAdapter(elem_path))
class TestHub:
def __init__(self):
self.hub = Hub()
elem_path = ":memory:"
bam_path = "tests/data/align.bam"
self.hub.connect(CoverageAdapter(bam_path), ElementAdapter(elem_path))
def setUp(self):
print "SETUP!"
def tearDown(self):
print "TEAR DOWN!"
def test_calculate(self):
# Test for normal depths
depths = [10, 11, 11, 12, 12, 13, 12, 12, 12, 11, 10, 8]
cutoff = 12
posCount = float(len(depths))
fun = lambda x: x >= cutoff
(cov_s, comp_s, __) = self.hub.calculate(depths, cutoff)
assert_equal(cov_s, sum(depths)/posCount)
assert_equal(comp_s, len(filter(fun, depths))/posCount)
# Test with 0 depth positions
depths = [0, 10, 0, 5, 0]
cutoff = 8
posCount = float(len(depths))
(cov_m, comp_m, __) = self.hub.calculate(depths, cutoff)
assert_equal(cov_m, sum(depths)/posCount)
assert_equal(comp_m, len(filter(fun, depths))/posCount)
# Test with all depths = 0, outside reads
depths = [0, 0, 0, 0, 0, 0]
(cov_o, comp_o, __) = self.hub.calculate(depths, 10)
assert_equal(cov_o, 0)
assert_equal(comp_o, 0)
def test_stringify(self):
# Test function stringifying and compressing level representations
depths = [1,2,2,3,5,5,6,7,7,7,7]
answer = "1|2|2|3|5|5|6|7|7|7|7"
compressed = self.hub.stringify(depths)
# Decompress the string and compare with the expected answer
assert_equal(zlib.decompress(compressed), answer)