def test_memoryLeaks(self):
sm = _getMemUsage()
for x in range(1000):
self.randArgs()
bindings.calcHeterodimer(
seq1=self.seq1,
seq2=self.seq2,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
temp_c=self.temp_c,
max_loop=self.max_loop,
)
sleep(0.1) # Pause for any GC
em = _getMemUsage()
print("\n\tMemory usage before 1k runs of calcHeterodimer: ", sm)
print("\tMemory usage after 1k runs of calcHeterodimer: ", em)
print("\t\t\t\t\tDifference: \t", em - sm)
if em - sm > 500:
raise AssertionError(
"Memory usage increase after 1k runs of \n\t"
"calcHeterodimer > 500 bytes -- potential \n\t"
"memory leak (mem increase: {})".format(em - sm)
)
def test_calcHeterodimer(self):
for _ in range(100):
self.randArgs()
binding_res = bindings.calcHeterodimer(
seq1=self.seq1,
seq2=self.seq2,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
temp_c=self.temp_c,
max_loop=self.max_loop,
output_structure=True
)
wrapper_res = wrappers.calcHeterodimer(
seq1=self.seq1,
seq2=self.seq2,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
temp_c=self.temp_c,
max_loop=self.max_loop
)
self.assertEqual(int(binding_res.tm), int(wrapper_res.tm))
self.assertEqual(
binding_res.ascii_structure,
wrapper_res.ascii_structure
)
# Ensure that order of sequences does not matter
# Should be fixed as of Primer3 2.3.7 update
binding_12_res = bindings.calcHeterodimer(
seq1=self.seq1,
seq2=self.seq2,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
temp_c=self.temp_c,
max_loop=self.max_loop,
output_structure=True
)
binding_21_res = bindings.calcHeterodimer(
seq1=self.seq1,
seq2=self.seq2,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
temp_c=self.temp_c,
max_loop=self.max_loop
)
self.assertEqual(int(binding_12_res.tm), int(binding_21_res.tm))
def test_calcHeterodimer(self):
for _ in range(25):
self.randArgs()
binding_res = bindings.calcHeterodimer(
seq1=self.seq1,
seq2=self.seq2,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
temp_c=self.temp_c,
max_loop=self.max_loop)
wrapper_res = wrappers.calcHeterodimer(
seq1=self.seq1,
seq2=self.seq2,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
temp_c=self.temp_c,
max_loop=self.max_loop)
if not wrapper_res:
self.assertTrue(binding_res == None)
else:
self.assertEqual(int(binding_res.tm), int(wrapper_res.tm))
def test_memoryLeaks(self):
sm = _getMemUsage()
for x in range(100):
self.randArgs()
bindings.calcHeterodimer(seq1=self.seq1,
seq2=self.seq2,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
temp_c=self.temp_c,
max_loop=self.max_loop)
sleep(0.1) # Pause for any GC
em = _getMemUsage()
print('\n\tMemory usage before 1k runs of calcHeterodimer: ', sm)
print('\tMemory usage after 1k runs of calcHeterodimer: ', em)
print('\t\t\t\t\tDifference: \t', em - sm)
if em - sm > 500:
raise AssertionError(
'Memory usage increase after 1k runs of \n\t'
'calcHeterodimer > 500 bytes -- potential \n\t'
'memory leak (mem increase: {})'.format(em - sm))
def test_calcHeterodimer(self):
for _ in range(25):
self.randArgs()
binding_res = bindings.calcHeterodimer(
seq1=self.seq1,
seq2=self.seq2,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
temp_c=self.temp_c,
max_loop=self.max_loop)
wrapper_res = wrappers.calcHeterodimer(
seq1=self.seq1,
seq2=self.seq2,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
temp_c=self.temp_c,
max_loop=self.max_loop)
self.assertEqual(int(binding_res.tm), int(wrapper_res.tm))
