def addPathways(self, bioPax, root, ns, verbose=False):
pathways = root.findall('bp:Pathway', ns)
for pw in pathways:
rdfID = pw.get("{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
pathwayComponents = pw.findall('bp:pathwayComponent', ns)
organism = pw.find('bp:organism', ns).get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource")
for biosource in root.findall("bp:BioSource", ns):
if biosource.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID"
) in organism:
organism = root.find("bp:BioSource",
ns).find("bp:name", ns).text
name = pw.findall('bp:name', ns)
displayName = pw.find('bp:displayName', ns).text
comment = pw.findall('bp:comment', ns)
xref = pw.findall('bp:xref', ns)
dataSource = pw.find('bp:dataSource', ns)
pathwaySteps = pw.findall('bp:pathwayOrder', ns)
newPathway = Pathway(rdfID, pathwayComponents, pathwaySteps,
organism, name, displayName, comment, xref,
dataSource)
bioPax.addPathway(newPathway)
if verbose:
print(ToString(newPathway))
def addFragmentFeatures(self, bioPax, root, ns, verbose=False):
features = root.findall("bp:FragmentFeature", ns)
for feature in features:
rdfID = feature.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
featureLocation = feature.find("bp:featureLocation", ns)
newFeature = FragmentFeature(rdfID, featureLocation)
bioPax.addFragmentFeature(newFeature)
if verbose:
print(ToString(newFeature))
def addPathwaySteps(self, bioPax, root, ns, verbose=False):
pathwaySteps = root.findall("bp:PathwayStep", ns)
for pathwayStep in pathwaySteps:
rdfID = pathwayStep.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
stepProcess = pathwayStep.findall(
"bp:stepProcess",
ns) #Pathway / BiochemicalReaction / Catalysis / Control
nextSteps = pathwayStep.findall("bp:nextStep", ns) #PathwayStep
newPathwayStep = PathwayStep(rdfID, stepProcess, nextSteps)
bioPax.addPathwayStep(newPathwayStep)
if verbose:
print(ToString(newPathwayStep))
def addSequenceSites(self, bioPax, root, ns, verbose=False):
sequenceSites = root.findall("bp:SequenceSite", ns)
for sequenceSite in sequenceSites:
rdfID = sequenceSite.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
sequencePosition = sequenceSite.find("bp:sequencePosition", ns)
positionStatus = sequenceSite.find("bp:positionStatus", ns)
newSequenceSite = SequenceSite(rdfID, sequencePosition,
positionStatus)
bioPax.addSequenceSite(newSequenceSite)
if verbose:
print(ToString(newSequenceSite))
def main():
foutPath = os.path.join(os.getcwd(), "outputs")
bpxParser = BioPaxParser.Parser()
inputFilePath = args.bioPaxFilePath
verbose = args.verbose
if os.path.exists(inputFilePath):
if os.path.isfile(inputFilePath):
if str.endswith(inputFilePath, ".xml"):
bioPax = bpxParser.parse(inputFilePath, verbose)
analyseBiochemicalReactionCollection(bioPax)
if verbose:
print(ToString(bioPax))
def addStoichiometries(self, bioPax, root, ns, verbose=False):
stoichiometries = root.findall("bp:Stoichiometry", ns)
for stoichiometry in stoichiometries:
rdfID = stoichiometry.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
stoichiometricCoefficient = stoichiometry.find(
"bp:stoichiometricCoefficient", ns)
physicalEntity = stoichiometry.find("bp:physicalEntity", ns)
newStoichiometry = Stoichiometry(rdfID, stoichiometricCoefficient,
physicalEntity)
bioPax.addStoichiometry(newStoichiometry)
if verbose:
print(ToString(newStoichiometry))
def addModificationFeatures(self, bioPax, root, ns, verbose=False):
""" Considered as FragmentFeatures """
modificationFeatures = root.findall("bp:ModificationFeature", ns)
for modification in modificationFeatures:
rdfID = modification.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
featureLocation = modification.find("bp:featureLocation", ns)
# add if necessary :
# modificationType = modification.find("bp:modificationType",ns)
# newFeature = ModificationFeature(rdfID,featureLocation,modificationType)
newFeature = FragmentFeature(rdfID, featureLocation)
bioPax.addFragmentFeature(newFeature)
if verbose:
print(ToString(newFeature))
def addSequenceIntervals(self, bioPax, root, ns, verbose=False):
intervals = root.findall("bp:SequenceInterval", ns)
for sequenceInterval in intervals:
rdfID = sequenceInterval.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
sequenceIntervalBegin = sequenceInterval.find(
"bp:featureLocation", ns)
sequenceIntervalEnd = sequenceInterval.find(
"bp:featureLocation", ns)
# .get("{http://www.biopax.org/release/biopax-level3.owl#}resource")
newSequenceInterval = SequenceInterval(rdfID,
sequenceIntervalBegin,
sequenceIntervalEnd)
bioPax.addSequenceInterval(newSequenceInterval)
if verbose:
print(ToString(newSequenceInterval))
def addControls(self, bioPax, root, ns, verbose=False):
controls = root.findall('bp:Control', ns)
for control in controls:
rdfID = control.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
controller = control.find("bp:controller", ns)
controlled = control.find("bp:controlled", ns)
controlType = control.find("bp:controlType", ns)
xref = control.findall("bp:xref", ns)
dataSource = control.find("bp:dataSource", ns)
newControl = Control(rdfID, controller, controlled, controlType,
xref, dataSource)
bioPax.addControl(newControl)
if verbose:
print(ToString(newControl))
def addSmallMolecules(self, bioPax, root, ns, verbose=False):
smallMolecules = root.findall('bp:SmallMolecule', ns)
for smallMolecule in smallMolecules:
rdfID = smallMolecule.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
entityReference = smallMolecule.find("bp:entityReference", ns)
name = smallMolecule.findall("bp:name", ns)
cellularLocation = smallMolecule.find("bp:cellularLocation", ns)
displayName = smallMolecule.find("bp:displayName", ns)
comment = smallMolecule.findall("bp:comment", ns)
xref = smallMolecule.findall("bp:xref", ns)
dataSource = smallMolecule.find("bp:dataSource", ns)
newSmallMolecule = SmallMolecule(rdfID, entityReference, name,
cellularLocation, displayName,
comment, xref, dataSource)
bioPax.addSmallMolecule(newSmallMolecule)
if verbose:
print(ToString(newSmallMolecule))
def addBiochemicalReactions(self, bioPax, root, ns, verbose=False):
BiochemicalReactions = root.findall('bp:BiochemicalReaction', ns)
for bioch in BiochemicalReactions:
rdfID = bioch.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
conversionDirection = bioch.find("bp:conversionDirection", ns)
left = bioch.findall("bp:left", ns)
right = bioch.findall("bp:right", ns)
displayName = bioch.find("bp:displayName", ns)
comment = bioch.findall("bp:comment", ns)
xref = bioch.findall("bp:xref", ns)
dataSource = bioch.find("bp:dataSource", ns)
newBiochemicalReaction = BiochemicalReaction(
rdfID, conversionDirection, left, right, displayName, comment,
xref, dataSource)
bioPax.addBiochemicalReaction(newBiochemicalReaction)
if verbose:
print(ToString(newBiochemicalReaction))
def addComplexes(self, bioPax, root, ns, verbose=False):
complexes = root.findall('bp:Complex', ns)
for cplx in complexes:
rdfID = cplx.get("{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
name = cplx.findall("bp:name", ns)
cellularLocation = cplx.find("bp:cellularLocation", ns)
displayName = cplx.find("bp:displayName", ns)
comment = cplx.findall("bp:comment", ns)
xref = cplx.findall("bp:xref", ns)
dataSource = cplx.find("bp:dataSource", ns)
memberPhysicalEntities = cplx.findall("bp:memberPhysicalEntities",
ns)
components = cplx.findall("bp:component", ns)
componentStoichiometries = cplx.findall(
"bp:componentStoichiometry", ns)
newComplex = Complex(rdfID, name, cellularLocation, displayName,
comment, xref, dataSource,
memberPhysicalEntities,
componentStoichiometries, components)
bioPax.addComplex(newComplex)
if verbose:
print(ToString(newComplex))
def addProteins(self, bioPax, root, ns, verbose=False):
proteins = root.findall('bp:Protein', ns)
for protein in proteins:
rdfID = protein.get(
"{http://www.w3.org/1999/02/22-rdf-syntax-ns#}ID")
cellularLocation = protein.find('bp:cellularLocation', ns)
displayName = protein.find("bp:displayName", ns)
comment = protein.findall("bp:comment", ns)
xref = protein.findall("bp:xref", ns)
dataSource = protein.find("bp:dataSource", ns)
entityReference = protein.find("bp:entityReference", ns)
feature = protein.findall("bp:feature", ns)
name = protein.findall("bp:name", ns)
memberPhysicalEntities = protein.findall(
"bp:memberPhysicalEntities", ns)
newProtein = Protein(rdfID, cellularLocation, displayName, comment,
xref, dataSource, entityReference, feature,
name, memberPhysicalEntities)
bioPax.addProtein(newProtein)
if verbose:
print(ToString(newProtein))