output.append(', '.join(cladeA.ncbiNames) + ':')
output.append('')
cladeAEcGraph = cladeA.coreMetabolism(majorityPercentageCoreMetabolism)
cladeAEcCount = len(cladeAEcGraph.getECs())
output.append('core metabolism ECs: ' + str(cladeAEcCount))
output.append('')
#- get "neofunctionalised" ECs
cladeANeofunctionalisedMetabolismSet = cladeA.neofunctionalisedECs(
majorityPercentageCoreMetabolism,
majorityPercentageNeofunctionalisation).getECs()
cladeASortedList = list(cladeANeofunctionalisedMetabolismSet)
cladeASortedList.sort()
#- calculate redundancy
cladeARedundancy = Redundancy(cladeAEcGraph)
cladeARedundancyContribution = RedundancyContribution(
cladeARedundancy, cladeANeofunctionalisedMetabolismSet)
cladeARobustECsForNeofunctionalisedEC = cladeARedundancyContribution.getContributedKeysForSpecial(
RedundancyType.ROBUSTNESS)
cladeAFlexibleECsForNeofunctionalisedEC = cladeARedundancyContribution.getContributedKeysForSpecial(
RedundancyType.TARGET_FLEXIBILITY)
#- REPEAT for each "neofunctionalised" EC
output.append('"neofunctionalised" ECs: ' + str(len(cladeASortedList)) +
' (' + str(
Percent.getPercentStringShort(len(cladeASortedList),
cladeAEcCount, 0)) + '%)')
for ecNumber in cladeASortedList:
#- print number of ECs the "neofunctionalised" EC provides redundancy for (robustness and flexibility)
output.append(
#- get Deltaproteobacteria
clade = getClade()
majorityPercentageCoreMetabolism = 80
output.append( 'core metabolism majority: ' + str(majorityPercentageCoreMetabolism) + '%' )
output.append('')
output.append(', '.join(clade.ncbiNames) + ':')
output.append('')
#- get ECs
cladeEcGraph = clade.coreMetabolism(majorityPercentageCoreMetabolism)
cladeEcCount = len(cladeEcGraph.getECs())
output.append( 'core metabolism ECs: ' + str(cladeEcCount) )
output.append('')
#- calculate redundancy
cladeRedundancy = Redundancy(cladeEcGraph)
#- print number of redundant ECs, including percentage of all ECs, for all types of redundancy
output.append('')
output.append( 'Robustness fully: ' + Percent.floatToPercentString(cladeRedundancy.getRedundancyRatio(RedundancyType.ROBUSTNESS) ) )
output.append( 'Robustness partial: ' + Percent.floatToPercentString(cladeRedundancy.getRedundancyRatio(RedundancyType.ROBUSTNESS_PARTIAL) ) )
output.append( 'Robustness both: ' + Percent.floatToPercentString(cladeRedundancy.getRedundancyRatio(RedundancyType.ROBUSTNESS_BOTH) ) )
output.append('')
output.append( 'Flexibility fully: ' + Percent.floatToPercentString(cladeRedundancy.getRedundancyRatio(RedundancyType.FLEXIBILITY) ) )
output.append( 'Flexibility partial: ' + Percent.floatToPercentString(cladeRedundancy.getRedundancyRatio(RedundancyType.FLEXIBILITY_PARTIAL) ) )
output.append( 'Flexibility both: ' + Percent.floatToPercentString(cladeRedundancy.getRedundancyRatio(RedundancyType.FLEXIBILITY_BOTH) ) )
output.append('')
output.append( 'Target-flexibility fully: ' + Percent.floatToPercentString(cladeRedundancy.getRedundancyRatio(RedundancyType.TARGET_FLEXIBILITY) ) )
output.append( 'Target-flexibility partial: ' + Percent.floatToPercentString(cladeRedundancy.getRedundancyRatio(RedundancyType.TARGET_FLEXIBILITY_PARTIAL) ) )
output.append( 'Target-flexibility both: ' + Percent.floatToPercentString(cladeRedundancy.getRedundancyRatio(RedundancyType.TARGET_FLEXIBILITY_BOTH) ) )
output.append('')
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)
#- calculate redundancy
cladeRedundancy = Redundancy(cladeEcGraph)
cladeRedundancyContribution = RedundancyContribution(
cladeRedundancy, cladeNeofunctionalisedMetabolismSet)
cladeRobustnessContributedECsForContributingNeofunctionalisedEC = cladeRedundancyContribution.getContributedKeysForSpecial(
redundancyType)
cladeRobustnessContributingNeofunctionalisedECs = set(
cladeRobustnessContributedECsForContributingNeofunctionalisedEC.keys())
#- REPEAT for each function change consisting of "neofunctionalised" ECs, which also contribute to redundancy
output.append(
'"neofunctionalised" ECs: ' +
str(len(cladeNeofunctionalisedMetabolismSet)) + ' (' + str(
Percent.getPercentStringShort(
len(cladeNeofunctionalisedMetabolismSet), cladeEcCount, 0)) +
'%)')
cladeEcCount = len(cladeEcGraph.getECs())
output.append('core metabolism ECs: ' + str(cladeEcCount))
output.append('')
#- calculate "neofunctionalised" ECs
cladeNeofunctionalisedMetabolismSet = clade.neofunctionalisedECs(
majorityPercentageCoreMetabolism,
majorityPercentageNeofunctionalisation,
eValue=eValue).getECs()
cladeNeofunctionalisationsForFunctionChange = clade.neofunctionalisationsForFunctionChange(
majorityPercentageCoreMetabolism,
majorityPercentageNeofunctionalisation,
eValue=eValue)
#- calculate redundancy
cladeRedundancy = Redundancy(cladeEcGraph)
cladeRedundancyContribution = RedundancyContribution(
cladeRedundancy, cladeNeofunctionalisedMetabolismSet)
cladeRobustnessContributedECsForContributingNeofunctionalisedEC = cladeRedundancyContribution.getContributedKeysForSpecial(
redundancyType)
cladeRobustnessContributingNeofunctionalisedECs = set(
cladeRobustnessContributedECsForContributingNeofunctionalisedEC.keys())
#- export graph of core metabolism, colouring the edges of (contributing) neofunctionalised ECs
edgesOfNeofunctionalisedECs = set()
for key in cladeNeofunctionalisedMetabolismSet:
for edge in cladeEcGraph.getEdgesFromKey(key):
edgesOfNeofunctionalisedECs.add(edge)
Export.addColourAttribute(cladeEcGraph,
Export.Colour.BLUE,