def test_Chromosome_binsize1_update_current_loci(self):
print("test_Chromosome_binsize1_update_current_loci")
c = Chromosome('testSample', 1, 'chr1')
c.update_current_loci(0)
c.update_current_loci(1)
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 3)
def test_Chromosome_binsize3_binEdgeBegins(self):
print("test_Chromosome_binsize3_binEdgeBegins")
c = Chromosome('testSample', 3, 'chr1')
for y, x in enumerate([0, 0, 1, 1], 1):
print(y)
c.update_current_loci(x)
self.assertEqual(len(c.LociList), 0)
def test_Chromosome_binsize3_binEdgeOutOfBounds(self):
print("test_Chromosome_binsize3_binEdgeOutOfBounds")
c = Chromosome('testSample', 3, 'chr1')
for y, x in enumerate([0, 0, 0, 0, 1, 1], 1):
print(y)
c.update_current_loci(x)
self.assertEqual(len(c.LociList), 1)
self.assertEqual(c.LociList[-1].start, 1)
self.assertEqual(c.LociList[-1].end, 2)
self.assertEqual(c.current_loci.start, 3)
self.assertEqual(c.current_loci.end, 7)
def test_Chromosome_binsize1_binBoundaries(self):
print("test_Chromosome_binsize1_binBoundaries")
c = Chromosome('testSample', 1, 'chr1')
for x in range(5):
c.update_current_loci(2)
c.update_current_loci(0)
for x in range(5):
c.update_current_loci(2)
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 12)
c.make_tidy()
self.assertEqual(c.current_loci.end, 11)
def test_Chromosome_reDefine_binBoundary_if_no_coverage_more_than_binEdge_but_less_than_binSize(
self):
print(
"test_Chromosome_reDefine_binBoundary_if_no_coverage_more_than_binEdge_but_less_than_binSize"
)
c = Chromosome('testSample', 5, 'chr1')
for y, x in enumerate([1, 1, 0, 0, 0, 0, 0, 0, 1, 1], 1):
print(y)
c.update_current_loci(x)
self.assertEqual(len(c.LociList), 1)
self.assertEqual(c.LociList[-1].start, 1)
self.assertEqual(c.LociList[-1].end, 5)
self.assertEqual(c.current_loci.start, 6)
self.assertEqual(c.current_loci.end, 11)
def test_Chromosome_binsize2_binBoundaries(self):
print("test_Chromosome_binsize2_binBoundaries")
c = Chromosome('testSample', 2, 'chr1')
self.assertEqual(c.binEdge, 1)
for x in [1, 0, 0, 1]:
#print(c.current_loci.start, c.current_loci.end)
c.update_current_loci(x)
for p in c.LociList:
print(p.start, p.end, p.LastCoveredBase)
print(c.current_loci.start, c.current_loci.end,
c.current_loci.LastCoveredBase)
self.assertEqual(c.current_loci.end, 5)
# self.assertEqual(c.
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(len(c.LociList), 0)
def test_Chromosome_zeroBin(self):
print("test_Chromosome_zeroBin")
c = Chromosome('testSample', 0, 'chr1')
self.assertEqual(c.sample, "testSample")
self.assertEqual(c.CHR, "chr1")
self.assertEqual(c.binEdge, 0)
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 1)
def test_Chromosome_zeroBin_update_current_loci(self):
print("test_Chromosome_zeroBin_update_current_loci")
c = Chromosome('testSample', 0, 'chr1')
c.update_current_loci(1) # add a base with depth 1
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 2)
c.update_current_loci(5) # add a base with depth 5
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 3)
c.update_current_loci(0) # add a base with depth 0
self.assertEqual(
c.LociList[-1].end,
2) # check the last loci end has been adjusted backwards
self.assertEqual(c.current_loci.start, 3)
self.assertEqual(c.current_loci.end, 4)
c.update_current_loci(0) # add another base with depth 0
self.assertEqual(c.current_loci.start, 3)
self.assertEqual(c.current_loci.end, 5)
def test_Chromosome_makes_empty_loci(self):
print("Chromosome_makes_empty_loci")
c = Chromosome('testSample', 0, 'chr1')
c.update_current_loci(0)
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 2)
c.update_current_loci(0)
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 3)
c.update_current_loci(0)
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 4)
c.update_current_loci(1)
self.assertEqual(
c.LociList[-1].end,
3) # check the last loci end has been adjusted backwards
self.assertEqual(c.current_loci.start, 4)
self.assertEqual(c.current_loci.end, 5)
def test_Chromosome_update_current_loci(self):
print("test_Chromosome_update_current_loci")
c = Chromosome('testSample', 10, 'chr1')
c.update_current_loci(1) # add a base with depth 1
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 2)
c.update_current_loci(5) # add a base with depth 5
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 3)
c.update_current_loci(0) # add a base with depth 0
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 4)
def test_Chromosome_binsize3_binBoundaries(self):
print("test_Chromosome_binsize3_binBoundaries")
c = Chromosome('testSample', 3, 'chr1')
self.assertEqual(len(c.LociList), 0)
self.assertEqual(c.binEdge, 2)
for y, x in enumerate([0, 1, 0, 0, 0], 1):
print(y, x)
c.update_current_loci(x)
# CHECKS BEFORE MERGE
self.assertEqual(c.current_loci.N_basesCovered, 0)
self.assertEqual(c.current_loci.end, 6)
self.assertEqual(c.current_loci.start, 5)
self.assertEqual(len(c.LociList), 1)
self.assertEqual(c.LociList[-1].LastCoveredBase, 2)
c.update_current_loci(1)
# # CHECKS AFTER MERGE
self.assertEqual(len(c.LociList), 0)
self.assertEqual(c.currentPosition, 7)
self.assertEqual(c.current_loci.start, 1)
self.assertEqual(c.current_loci.end, 7)
self.assertEqual(c.current_loci.N_basesCovered, 2)
self.assertEqual(c.current_loci.depthSum, 2)
self.assertEqual(c.current_loci.FirstCoveredBase, 2)
self.assertEqual(c.current_loci.LastCoveredBase, 6)