"""
A unit test for the creation of collective enzyme graphs by using an EC majority.
Two methods of doing so are compared and must always return the same value.
At last, the identity of included enzymes is compared, which must result in *0*.
Warnings
--------
The first result is time-dependant! It will certainly change on future updates of KEGG. However, it should be somewhere around *184*.
"""
import unittest
from FEV_KEGG.KEGG import Organism
import FEV_KEGG
[docs]class Test(unittest.TestCase):
[docs] def test_majorityEcGraph_difference(self):
FEV_KEGG.startProcessPool()
enterobacteriales_organisms_abbreviations = ['eco', 'ses', 'sfl', 'ent', 'esa', 'kpn', 'cko', 'ype', 'spe', 'buc']
enterobacteriales_organisms = Organism.Group(organismAbbreviations = enterobacteriales_organisms_abbreviations)
enterobacteriales_organisms_abbreviations = ['eco', 'ses', 'sfl', 'ent', 'esa', 'kpn', 'cko', 'ype', 'spe', 'buc']
gammaproteobacteria_organisms_abbreviations = ['hin', 'mht', 'xcc', 'vch', 'pae', 'acb', 'son', 'pha', 'amc', 'lpn', 'ftu', 'aha']
gammaproteobacteria_organisms_abbreviations.extend(enterobacteriales_organisms_abbreviations) # extend with the sub-set, because they are also part of the set
gammaproteobacteria_organisms = Organism.Group(organismAbbreviations = gammaproteobacteria_organisms_abbreviations)
enterobacteriales_EC_graph = enterobacteriales_organisms.majorityEcGraph(majorityPercentage = 80, noMultifunctional = True)
gammaproteobacteria_EC_graph = gammaproteobacteria_organisms.majorityEcGraph(majorityPercentage = 80, noMultifunctional = True)
enterobacteriales_EC_set = enterobacteriales_EC_graph.getECs()
gammaproteobacteria_EC_set = gammaproteobacteria_EC_graph.getECs()
only_enterobacteriales_EC_set = enterobacteriales_EC_set.difference(gammaproteobacteria_EC_set)
output = []
for ec in only_enterobacteriales_EC_set:
output.append(ec.__str__())
result = len(output)
print(str(result) + ' results')
self.assertEqual(result, 184)
enterobacteriales_enzyme_graph = enterobacteriales_organisms.collectiveEnzymeGraphByEcMajority(majorityPercentage = 80, noMultifunctional = True)
gammaproteobacteria_enzyme_graph = gammaproteobacteria_organisms.collectiveEnzymeGraphByEcMajority(majorityPercentage = 80, noMultifunctional = True)
enterobacteriales_enzyme_graph.removeMultifunctionalEnzymes()
gammaproteobacteria_enzyme_graph.removeMultifunctionalEnzymes()
enterobacteriales_enzymes = enterobacteriales_enzyme_graph.getEnzymes()
gammaproteobacteria_enzymes = gammaproteobacteria_enzyme_graph.getEnzymes()
enterobacteriales_EC_set_2 = set()
for enzyme in enterobacteriales_enzymes:
ecNumbers = enzyme.ecNumbers
enterobacteriales_EC_set_2.update(ecNumbers)
gammaproteobacteria_EC_set_2 = set()
for enzyme in gammaproteobacteria_enzymes:
ecNumbers = enzyme.ecNumbers
gammaproteobacteria_EC_set_2.update(ecNumbers)
only_enterobacteriales_EC_set_2 = enterobacteriales_EC_set_2.difference(gammaproteobacteria_EC_set_2)
output = []
for ec in only_enterobacteriales_EC_set_2:
output.append(ec.__str__())
result2 = len(output)
print(str(result2) + ' results')
self.assertEqual(result2, result)
output = []
for ec in only_enterobacteriales_EC_set_2.symmetric_difference(only_enterobacteriales_EC_set):
output.append(ec.__str__())
result3 = len(output)
print(str(result3) + ' results')
self.assertEqual(result3, 0)
for ecString in output:
print( ecString )
if __name__ == "__main__":
unittest.main()