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." )