if __name__ == '__main__':
#- Get all metabolic pathways of all E. coli organisms from KEGG.
eColiOrganisms = FEV_KEGG.KEGG.Organism.Group(
searchString='Escherichia coli K-12').organisms
#- For each organism, combine all pathways to the metabolic network, by UNION operation.
organismEcGraphs = []
for organism in eColiOrganisms:
organismPathways = organism.getMetabolicPathways()
organismSubstanceReactionGraph = SubstanceReactionGraph.fromPathway(
organismPathways)
#- Convert this metabolic network into a substance-ecNumber graph.
organismSubstanceGeneGraph = SubstanceGeneGraph.fromSubstanceReactionGraph(
organismSubstanceReactionGraph)
organismSubstanceEcGraph = SubstanceEcGraph.fromSubstanceGeneGraph(
organismSubstanceGeneGraph)
organismEcGraphs.append(organismSubstanceEcGraph)
firstGraph = organismEcGraphs.pop(0)
#- Combine all organisms' networks to a consensus network, by INTERSECT operation, leaving only substances and EC numbers that occur in all organisms.
intersectedEcGraph = firstGraph
intersectedEcGraph = intersectedEcGraph.intersection(organismEcGraphs)
#- Print all EC numbers that occur in all organisms.
output = []
for ecNumber in intersectedEcGraph.getECs():
output.append(ecNumber.__str__())
if __name__ == '__main__':
#- Get all known pathways of eco and sso from KEGG.
eco = FEV_KEGG.KEGG.Organism.Organism('eco')
sso = FEV_KEGG.KEGG.Organism.Organism('sso')
ecoPathways = eco.getMetabolicPathways()
ssoPathways = sso.getMetabolicPathways()
#- Convert each pathway into a substance-ecNumber graph. This is the incomplete metabolic network.
ecoReactionGraph = SubstanceReactionGraph.fromPathway(ecoPathways)
ssoReactionGraph = SubstanceReactionGraph.fromPathway(ssoPathways)
ecoGeneGraph = SubstanceGeneGraph.fromSubstanceReactionGraph(ecoReactionGraph)
ssoGeneGraph = SubstanceGeneGraph.fromSubstanceReactionGraph(ssoReactionGraph)
ecoEnzymeGraph = SubstanceEnzymeGraph.fromSubstanceGeneGraph(ecoGeneGraph)
ssoEnzymeGraph = SubstanceEnzymeGraph.fromSubstanceGeneGraph(ssoGeneGraph)
#- Remove multifunctional enzymes, meaning enzymes associated with more than one EC number. Helps to reduce false gene duplications.
ecoEnzymeGraph.removeMultifunctionalEnzymes()
ssoEnzymeGraph.removeMultifunctionalEnzymes()
ecoEcGraph = SubstanceEcGraph.fromSubstanceEnzymeGraph(ecoEnzymeGraph)
ssoEcGraph = SubstanceEcGraph.fromSubstanceEnzymeGraph(ssoEnzymeGraph)
#- Combine both species' networks to a consensus network, by INTERSECTION operation.
intersectionEcGraph = ecoEcGraph.intersection(ssoEcGraph)
from FEV_KEGG.KEGG.Organism import Organism
if __name__ == '__main__':
#- Download pathway definition as KGML.
eco = Organism('eco')
eco00260 = eco.getPathway('00260')
eco01100 = eco.getPathway('01100')
#- Convert to substance-reaction graph.
eco00260_reactionGraph = SubstanceReactionGraph.fromPathway(eco00260)
eco01100_reactionGraph = SubstanceReactionGraph.fromPathway(eco01100)
#- Convert to substance-gene graph
eco00260_geneGraph = SubstanceGeneGraph.fromSubstanceReactionGraph(
eco00260_reactionGraph)
eco01100_geneGraph = SubstanceGeneGraph.fromSubstanceReactionGraph(
eco01100_reactionGraph)
#- Convert to substance-enzyme graph
eco00260_enzymeGraph = SubstanceEnzymeGraph.fromSubstanceGeneGraph(
eco00260_geneGraph)
eco01100_enzymeGraph = SubstanceEnzymeGraph.fromSubstanceGeneGraph(
eco01100_geneGraph)
#- Get set of enzymes for each graph.
eco00260_enzymes = eco00260_enzymeGraph.getEnzymes()
eco01100_enzymes = eco01100_enzymeGraph.getEnzymes()
#- Calculate difference of enzyme sets.
difference_enzymes = eco00260_enzymes.difference(eco01100_enzymes)
if __name__ == '__main__':
#- Download pathway description as KGML.
eco = Organism('eco')
eco01100 = eco.getPathway('01100')
allNonOverviewPathways = eco.getMetabolicPathways(
includeOverviewMaps=False)
#- Convert to substance-reaction graph.
eco01100_reactionGraph = SubstanceReactionGraph.fromPathway(eco01100)
allNonOverviewPathways_reactionGraph = SubstanceReactionGraph.fromPathway(
allNonOverviewPathways)
#- Convert to substance-gene graph.
eco01100_geneGraph = SubstanceGeneGraph.fromSubstanceReactionGraph(
eco01100_reactionGraph)
allNonOverviewPathways_geneGraph = SubstanceGeneGraph.fromSubstanceReactionGraph(
allNonOverviewPathways_reactionGraph)
#- Convert to substance-ec graph.
eco01100_ecGraph = SubstanceEcGraph.fromSubstanceGeneGraph(
eco01100_geneGraph)
allNonOverviewPathways_ecGraph = SubstanceEcGraph.fromSubstanceGeneGraph(
allNonOverviewPathways_geneGraph)
#- Get set of EC numbers for each graph.
eco01100_ecNumbers = eco01100_ecGraph.getECs()
allNonOverviewPathways_ecNumbers = allNonOverviewPathways_ecGraph.getECs()
#- Calculate difference of EC number sets.
difference_ecNumbers = eco01100_ecNumbers.difference(