nfolds = argData['crossval_folds'] # applicable for average CV
#Nodes
nodes = [ProteinInteractionNode, KeggNode, ReactomeNode, GoNode, InterproNode]
#staticFeatures = []
staticFeatures = argData['static_data'].split(',')
logging.info(staticFeatures)
logging.info("--- USING {0} METAPATH FEATURE SETS".format(len(nodes)))
logging.info("--- USING {0} STATIC FEATURE SETS".format(len(staticFeatures)))
#fetch the description of proteins and pathway_ids
dbAdapter = OlegDB()
idDescription = dbAdapter.fetchPathwayIdDescription() #fetch the description
idNameSymbol = dbAdapter.fetchSymbolForProteinId(
) #fetch name and symbol for protein
if fileData is not None:
#logging.info("FOUND {0} POSITIVE LABELS".format(len(fileData[True])))
#logging.info("FOUND {0} NEGATIVE LABELS".format(len(fileData[False])))
trainData = metapathFeatures(disease,
currentGraph,
nodes,
idDescription,
staticFeatures,
loadedLists=fileData).fillna(0)
else:
trainData = metapathFeatures(disease, currentGraph, nodes, idDescription,
staticFeatures).fillna(0)
'''
# directory and file name for the ML Model
if isinstance(n, str) and n[0:3] == "GO:"
]
logging.info("GO nodes: %d" % (len(goNodes)))
interNodes = [
n for n in list(pdg.graph.nodes)
if isinstance(n, str) and n[0:3] == "IPR"
]
logging.info("INTERPRO nodes: %d" % (len(interNodes)))
# pfamNodes = [n for n in list(pdg.graph.nodes) if isinstance(n, str) and n[0:2]=="PF"]
# logging.info("Pfam nodes: %d"%(len(pfamNodes)))
# prositeNodes = [n for n in list(pdg.graph.nodes) if isinstance(n, str) and n[0:2]=="PS"]
# logging.info("PROSITE nodes: %d"%(len(prositeNodes)))
# Fetch node/edge information from db.
idDescription = dbad.fetchPathwayIdDescription()
idSymbol = dbad.fetchSymbolForProteinId()
try:
idUniprot = dbad.fetchUniprotForProteinId()
except Exception as e:
logging.error("No Uniprot in OlegDB: {0}".format(e))
idUniprot = {}
# add name, symbol and uniprot id to graph nodes
for n in pdg.graph.nodes:
if n in idUniprot:
pdg.graph.nodes[n]['UniprotId'] = idUniprot[n]
else:
pdg.graph.nodes[n]['UniprotId'] = ''
if n in idSymbol:
pdg.graph.nodes[n]['Symbol'] = idSymbol[n]
else: