clade = Clade('Archaea')
# pre-fetch collective metabolism into memory
clade.collectiveMetabolism(
excludeMultifunctionalEnzymes=settings.defaultNoMultifunctional)
# pre-fetch collective enzyme metabolism into memory
clade.collectiveMetabolismEnzymes(
excludeMultifunctionalEnzymes=settings.defaultNoMultifunctional)
return clade
if __name__ == '__main__':
#- get clade
clade = getClade()
majorityPercentageCoreMetabolism = 80
majorityPercentageNeofunctionalisation = 0
#- get neofunctionalisations
neofunctionalisationsForFunctionChange = clade.neofunctionalisationsForFunctionChange(
majorityPercentageCoreMetabolism,
majorityPercentageNeofunctionalisation)
#- export to HTML, including links and further info
dictToHtmlFile(neofunctionalisationsForFunctionChange,
clade.ncbiNames[0] +
'_Neofunctionalisations-For-FunctionChange.html',
byValueFirst=False,
inCacheFolder=True,
addEcDescriptions=True)
allNeofunctionalisations = set(
) # set of all neofunctionalisations, no matter which function change they belong to
for valueSet in neofunctionalisationsForFunctionChange.values():
allNeofunctionalisations.update(valueSet)
output.append('')
output.append('All neofunctionalisations: ' +
str(len(allNeofunctionalisations)))
#- print them into nice HTML
ecNumbers = set()
for functionChange in neofunctionalisationsForFunctionChange.keys():
ecNumbers.update(functionChange.ecPair)
dictToHtmlFile(neofunctionalisationsForFunctionChange,
clade.ncbiNames[0] +
'_Neofunctionalisations-For-FunctionChange.html',
byValueFirst=False,
inCacheFolder=True,
addEcDescriptions=ecNumbers)
output.append('\t[see ' + clade.ncbiNames[0] +
'_Neofunctionalisations-For-FunctionChange.html]')
output.append('')
#- calculate "neofunctionalised" ECs
cladeNeofunctionalisedMetabolismSet = clade.neofunctionalisedECs(
majorityPercentageCoreMetabolism,
majorityPercentageNeofunctionalisation,
eValue=eValue).getECs()
cladeNeofunctionalisationsForFunctionChange = clade.neofunctionalisationsForFunctionChange(
majorityPercentageCoreMetabolism,
majorityPercentageNeofunctionalisation,
eValue=eValue)
output.append('')
neofunctionalisationsForContributedEC = dict()
for neofunctionalisation, contributedECs in robustnessContributingNeofunctionalisations.items():
for contributedEC in contributedECs:
currentSetOfNeofunctionalisations = neofunctionalisationsForContributedEC.get(contributedEC, None)
if currentSetOfNeofunctionalisations is None:
currentSetOfNeofunctionalisations = set()
neofunctionalisationsForContributedEC[contributedEC] = currentSetOfNeofunctionalisations
currentSetOfNeofunctionalisations.add(neofunctionalisation)
ecNumbers = set()
for contributedEC in neofunctionalisationsForContributedEC.keys():
ecNumbers.add( contributedEC )
dictToHtmlFile(neofunctionalisationsForContributedEC, clade.ncbiNames[0] + '_' + redundancyType.name + '_Neofunctionalisations-For-Contributed-EC.html', byValueFirst=False, inCacheFolder=True, addEcDescriptions = ecNumbers)
for line in output:
print( line )