def __init__(self):
# given
self.query = "GTAGGCGAGATGACGCCAT"
self.targets = ["GTAGGCGAGTCCCGTTTATA", "CCACAGAAGATGACGCCATT"]
# when
self.t = Tesserae(mem_limit=False)
self.p = self.t.align(self.query, self.targets)
def test_mosaic_alignment_on_medium_queries_and_two_templates(self):
random.seed(0)
# given
for total_len in [100, 200, 500]:
partial_len = int(total_len / 2)
query = random_dna_string(total_len)
targets = ["".join(query[0:partial_len]) + random_dna_string(partial_len),
random_dna_string(partial_len) + "".join(query[partial_len:total_len])]
# when
t = Tesserae()
p = t.align(query, targets)
# then
assert len(p) == 3
assert p[1][0] == 'template0'
assert p[1][1] == "".join(targets[0][0:partial_len])
assert p[1][2] == 0
assert p[1][3] == partial_len - 1
assert p[2][0] == 'template1'
assert p[2][1] == repeat(" ", partial_len) + targets[1][partial_len:total_len]
assert p[2][2] == partial_len
assert p[2][3] == total_len - 1
def test_mosaic_alignment_on_medium_queries_and_two_templates(self):
# given
for total_len, (query, targets) in self.samples.items():
# when
t = Tesserae(mem_limit=False)
p = t.align(query, targets)
# then
self.__assertions__(p, targets, total_len)
def test_mosaic_alignment_on_medium_queries_and_two_templates_reduced_memory_usage(
self):
# given
for total_len, (query, targets) in self.samples.items():
# when
t = Tesserae(mem_limit=True)
p = t.align(query, targets)
max_mem_limit = sqrt(total_len) + 2
# then
self.__assertions__(p, targets, total_len)
assert t.traceback_limit <= max_mem_limit
assert t.states_to_save <= max_mem_limit
def test_mosaic_alignment_on_short_query_and_two_templates_reduced_memory_usage(
self):
# when
t = Tesserae(mem_limit=True)
p = t.align(self.query, self.targets)
max_mem_limit = sqrt(len(self.query)) + 1
# then
assert p == self.p
assert t.llk >= -27
assert t.llk <= -26
assert t.traceback_limit <= max_mem_limit
assert t.states_to_save <= max_mem_limit
def test_mosaic_alignment_on_short_query_and_two_templates(self):
# given
query = "GTAGGCGAGATGACGCCAT"
targets = ["GTAGGCGAGTCCCGTTTATA", "CCACAGAAGATGACGCCATT"]
# when
t = Tesserae()
p = t.align(query, targets)
# then
assert len(p) == 3
assert p[1][0] == 'template0'
assert p[1][1] == 'GTAGGCG'
assert p[1][2] == 0
assert p[1][3] == 6
assert p[2][0] == 'template1'
assert p[2][1] == ' AGATGACGCCAT'
assert p[2][2] == 7
assert p[2][3] == 18
class TestTesserae:
def __init__(self):
# given
self.query = "GTAGGCGAGATGACGCCAT"
self.targets = ["GTAGGCGAGTCCCGTTTATA", "CCACAGAAGATGACGCCATT"]
# when
self.t = Tesserae(mem_limit=False)
self.p = self.t.align(self.query, self.targets)
def test_mosaic_alignment_on_short_query_and_two_templates(self):
# then
assert len(self.p) == 3
assert self.p[1][0] == 'template0'
assert self.p[1][1] == 'GTAGGCG'
assert self.p[1][2] == 0
assert self.p[1][3] == 6
assert self.p[2][0] == 'template1'
assert self.p[2][1] == ' AGATGACGCCAT'
assert self.p[2][2] == 7
assert self.p[2][3] == 18
assert self.t.llk >= -27
assert self.t.llk <= -26
def test_mosaic_alignment_on_short_query_and_two_templates_reduced_memory_usage(
self):
# when
t = Tesserae(mem_limit=True)
p = t.align(self.query, self.targets)
max_mem_limit = sqrt(len(self.query)) + 1
# then
assert p == self.p
assert t.llk >= -27
assert t.llk <= -26
assert t.traceback_limit <= max_mem_limit
assert t.states_to_save <= max_mem_limit