def test_mean_otu_pct_abundance(self):
"""
Testing mean_otu_pct_abundance() function of biom_calc.py.
:return: Returns OK, if testing goal was achieved, otherwise raises
error.
"""
self.rel_a = bc.relative_abundance(self.biom)
self.result = bc.mean_otu_pct_abundance(
self.rel_a, ['GG_OTU_1','GG_OTU_2']
)
# Obtaining lists of function calculations and manual hand calculations
func_calc = self.result.values()
result1 = self.rel_a.values() # result1 is a list
# list containing hand calculated relative abundance values
hand_calc = [0.25/6, (1.0+0.3333333333333333+0.25+0.7142857142857143+0.3333333333333333)/6]
# Testing the validity of the calculations of mean_otu_pct_abundance().
for hand, res in zip(hand_calc, func_calc):
self.assertAlmostEqual(
hand*100, res,
msg='Mean OTU not calculated accurately.'
)
def test_MRA(self):
"""
Testing mean relative abundance calculation, MRA() function
of biom_calc.py.
:return: Returns OK, if testing goal was achieved, otherwise
raises error.
"""
self.result = bc.MRA(self.biom)
self.mean_otu = bc.mean_otu_pct_abundance(
bc.relative_abundance(self.biom),
['GG_OTU_1', 'GG_OTU_2', 'GG_OTU_3', 'GG_OTU_4', 'GG_OTU_5']
)
# Obtaining lists of function calculations and
# manual hand calculations
func_calc = self.result.values()
hand_calc = self.mean_otu.values()
# Testing the validity of the calculations of mean_otu_pct_abundance().
for hand, res in zip(hand_calc, func_calc):
self.assertAlmostEqual(
hand, res,
msg='Mean OTU not calculated accurately.'
)
def test_mean_otu_pct_abundance(self):
"""
Testing mean_otu_pct_abundance() function of biom_calc.py.
:return: Returns OK, if testing goal was achieved, otherwise raises
error.
"""
self.rel_a = bc.relative_abundance(self.biomf)
self.result = bc.mean_otu_pct_abundance(
self.rel_a, ["GG_OTU_1", "GG_OTU_2"]
)
# Obtaining lists of function calculations and manual hand calculations
func_calc = self.result.values()
# list containing hand calculated relative abundance values
hand_calc = [(0 + 0.0153846153846 + 0.0285714285714 + 0.04 + 0.05 +
0.0588235294118)/6,
(0.1 + 0.107692307692 + 0.114285714286 + 0.12 + 0.125 +
0.129411764706)/6]
# Testing the validity of the calculations of mean_otu_pct_abundance().
for hand, res in zip(hand_calc, func_calc):
self.assertAlmostEqual(
hand*100, res,
msg="Mean OTU not calculated accurately."
)
def test_mean_otu_pct_abundance(self):
"""
Testing mean_otu_pct_abundance() function of biom_calc.py.
:return: Returns OK, if testing goal was achieved, otherwise raises error.
"""
self.rel_a = bc.relative_abundance(self.biomf)
self.result = bc.mean_otu_pct_abundance(self.rel_a, ["GG_OTU_1", "GG_OTU_2"])
# list containing hand calculated relative abundance values
hand_calc = {"GG_OTU_1": 14.52348298, "GG_OTU_2": 15.73217761,
"GG_OTU_3": 26.58131438, "GG_OTU_4": 22.91732137,
"GG_OTU_5": 20.24570366}
# Testing the validity of the calculations of mean_otu_pct_abundance().
for oid in ["GG_OTU_1", "GG_OTU_2"]:
self.assertAlmostEqual(
hand_calc[oid], self.result[oid],
msg="Mean OTU percent abundance not calculated accurately."
)
