def test_correctionMethods(self):
self.randArgs()
for sc_method in ['schildkraut', 'santalucia', 'owczarzy']:
for tm_method in ['breslauer', 'santalucia']:
binding_tm = bindings.calcTm(seq=self.seq1,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
tm_method=tm_method,
salt_corrections_method=sc_method)
wrapper_tm = wrappers.calcTm(seq=self.seq1,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
tm_method=tm_method,
salt_corrections_method=sc_method)
self.assertEqual(int(binding_tm), int(wrapper_tm))
self.assertRaises(ValueError,
bindings.calcTm,
seq=self.seq1,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
tm_method='not_a_tm_method')
def test_correctionMethods(self):
self.randArgs()
for sc_method in ["schildkraut", "santalucia", "owczarzy"]:
for tm_method in ["breslauer", "santalucia"]:
binding_tm = bindings.calcTm(
seq=self.seq1,
mv_conc=int(self.mv_conc),
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=int(self.dna_conc),
tm_method=tm_method,
salt_corrections_method=sc_method,
)
wrapper_tm = wrappers.calcTm(
seq=self.seq1,
mv_conc=int(self.mv_conc),
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=int(self.dna_conc),
tm_method=tm_method,
salt_corrections_method=sc_method,
)
self.assertEqual(int(binding_tm), int(wrapper_tm))
self.assertRaises(
ValueError,
bindings.calcTm,
seq=self.seq1,
mv_conc=int(self.mv_conc),
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=int(self.dna_conc),
tm_method="not_a_tm_method",
)
def test_correctionMethods(self):
self.randArgs()
for sc_method in ['schildkraut', 'santalucia', 'owczarzy']:
for tm_method in ['breslauer', 'santalucia']:
binding_tm = bindings.calcTm(
seq=self.seq1,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
tm_method=tm_method,
salt_corrections_method=sc_method)
wrapper_tm = wrappers.calcTm(
seq=self.seq1,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
tm_method=tm_method,
salt_corrections_method=sc_method)
self.assertEqual(int(binding_tm), int(wrapper_tm))
self.assertRaises(ValueError, bindings.calcTm,
seq=self.seq1,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc,
tm_method='not_a_tm_method')
def test_calcTm(self):
for x in range(100):
self.randArgs()
binding_tm = bindings.calcTm(seq=self.seq1,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc)
wrapper_tm = wrappers.calcTm(seq=self.seq1,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc)
self.assertEqual(int(binding_tm), int(wrapper_tm))
def test_calcTm(self):
for x in range(25):
self.randArgs()
binding_tm = bindings.calcTm(
seq=self.seq1,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc)
wrapper_tm = wrappers.calcTm(
seq=self.seq1,
mv_conc=self.mv_conc,
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=self.dna_conc)
self.assertEqual(int(binding_tm), int(wrapper_tm))
def test_calcTm(self):
for x in range(25):
self.randArgs()
# The oligotm executable requires mv_conc and dna_conc to be ints
# (technically longs... see oligotm_main.c vs. oligotm.c
# discrepency)
binding_tm = bindings.calcTm(
seq=self.seq1,
mv_conc=int(self.mv_conc),
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=int(self.dna_conc))
wrapper_tm = wrappers.calcTm(
seq=self.seq1,
mv_conc=int(self.mv_conc),
dv_conc=self.dv_conc,
dntp_conc=self.dntp_conc,
dna_conc=int(self.dna_conc))
self.assertEqual(int(binding_tm), int(wrapper_tm))
