def setUp(self):
if os.path.exists("/tmp/test.flat"):
os.remove("/tmp/test.flat")
self.t = glbase3.flat_track(filename="/tmp/test.flat",
new=True,
name="Test Track",
bin_format="f")
chr1 = [0] * 500
chr2 = [0] * 120
for i in range(100):
chr1[
i] = i # self.t.add_score(chromosome=1, left=i, right=i+1, score=i)
for i in range(100, 110):
chr2[
i] = i # self.t.add_score(chromosome=2, left=i, right=i+1, score=0)
chr2[
111] = 2 # self.t.add_score(chromosome=2, left=111, right=112, score=2)
chr2[
99] = 2 # self.t.add_score(chromosome=2, left=99, right=100, score=2)
self.t.add_chromosome_array(chromosome='1', arr=numpy.array(chr1))
self.t.add_chromosome_array(chromosome='2', arr=numpy.array(chr2))
self.t.finalise()
self.t = glbase3.flat_track(filename="/tmp/test.flat",
new=False,
name="Test Track",
bin_format="f")
def test_meta_data(self):
t = glbase3.flat_track(filename="/tmp/test.flat",
new=False,
name="Test Track",
bin_format="f")
self.assertEqual(t["name"], "Test Track")
self.assertEqual(t["bin_format"], "f")
def test_reload(self):
t = glbase3.flat_track(filename="/tmp/test.flat", bin_format="f")
a = self.t.get(glbase3.location(loc="chr1:0-100"))
expected_result = [i for i in range(100)] + [0]
self.assertTrue(False not in [
int(x) == int(y) for x, y in zip(a, expected_result)
]) # all seqs.
def test_mask(self):
t = glbase3.flat_track(filename="/tmp/test.flat", bin_format="f")
a = t.get(glbase3.location(loc="chr2:99-111"))
unmasked = [2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,2]
self.assertTrue(False not in [int(x) == int(y) for x, y in zip(a, unmasked)]) # all seqs.
a = t.get(glbase3.location(loc="chr2:99-111"), mask_zero=True)
expected = "[2.0 -- -- -- -- -- -- -- -- -- -- --]" # not sure how to test this apart from a string.
self.assertEqual(str(a), expected)
def test_pileup_no_respect_strand(self):
t = glbase3.flat_track(filename="/tmp/test.flat", bin_format="f")
g = glbase3.genelist(filename="test_data/track_test.bed", format=glbase3.format.bed).pointify().expand('loc', 15)
L, _ = t.pileup(genelists=g, filename="test_images/test_output_no_strand.png", bandwidth=15, respect_strand=False)
expected_result = numpy.array(list(range(0, 30)))
self.assertListEqual(list(L['track_test']), list(expected_result))
def setUp(self):
self.t = glbase3.flat_track(filename="/tmp/test.flat", new=True, name="Test Track", bin_format="f")
for i in range(0, 100):
self.t.add_score(chromosome=1, left=i, right=i+1, score=i)
for i in range(100,110):
self.t.add_score(chromosome=2, left=i, right=i+1, score=0)
self.t.add_score(chromosome=2, left=111, right=112, score=2)
self.t.add_score(chromosome=2, left=99, right=100, score=2)
self.t.finalise()
def test_pileup_respect_strand(self):
t = glbase3.flat_track(filename="/tmp/test.flat", bin_format="f")
g = glbase3.genelist(filename="test_data/track_test.bed", format=glbase3.format.bed).pointify().expand('loc', 15)
L, _ = t.pileup(genelists=g, filename="test_images/test_output_respect_strand.png", bandwidth=15, respect_strand=True)
expected_result = numpy.zeros(30)
expected_result += 14.5
# IF respect strand is true then you will get 4 arrays --> --> and <-- <-- the average of the 4
# will be 14.5 for all points.
# Note this is identical to the above test_draw_pielup()
# except respect_strand=False
self.assertListEqual(list(L['track_test']), list(expected_result))
def test_name_override(self):
t = glbase3.flat_track(filename="/tmp/test.flat", new=False, name="Changed Name", bin_format="f")
self.assertEqual(t["name"], "Changed Name")