class TestCoverageAdapter:
def __init__(self):
bam_path = "tests/data/align.bam"
self.adapter = CoverageAdapter(bam_path)
# These are the main results from "align.bam"
self.depths = [2., 4., 5., 5., 5., 5., 6., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 8., 8., 7., 7., 7., 7., 7., 7., 7., 6., 4., 4., 3., 3., 2., 2.]
def setUp(self):
print "SETUP!"
def tearDown(self):
print "TEAR DOWN!"
def test_read(self):
# Read BAM from position [1,10]
depths = self.adapter.read("chr1", 0, 9)
# Make assertions: we expect the read depths from 1st to 10th pos to be
# included.
answer = self.depths[0:10]
assert_equal(list(depths), answer)
# Test also an interval that extends beyond the reads
depths = self.adapter.read("chr1", 35, 45)
assert_equal(list(depths), self.depths[35:] + [0, 0, 0, 0, 0, 0, 0])
# Test interval completely outside the reads
depths = self.adapter.read("chr1", 50, 60)
assert_equal(list(depths), [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
# Test submitting a false chromosome ID
try:
bgi = self.adapter.read("crh1", 10, 20)
except ValueError, e:
assert_true(e.message == "invalid reference `crh1`")
def __init__(self):
bam_path = "tests/data/align.bam"
self.adapter = CoverageAdapter(bam_path)
# These are the main results from "align.bam"
self.depths = [2., 4., 5., 5., 5., 5., 6., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 7., 8., 8., 7., 7., 7., 7., 7., 7., 7., 6., 4., 4., 3., 3., 2., 2.]
