if compound_id not in nodes:
cpdName = compound_id
if compound_id in compoundNames:
cpdName = compoundNames[compound_id]
importer.add_node(['_Network_Node', 'Compound'], compound_id,
{'name': cpdName, 'idType': 'KEGG_COMPOUND',
'url': 'http://www.kegg.jp/dbget-bin/www_bget?cpd:' + compound_id})
# node = Node('NETWORK_NODE', 'Compound', id=name, idType='KEGG_COMPOUND', name=name)
# n = batch.create(node)
nodes.add(compound_id)
if compound.id not in compoundDict:
compoundDict[compound.id] = compound_id
currentNodes.add(compound_id)
importer.done_nodes()
for reaction in pathway.reactions:
if reaction.name in reactionToNode:
gene_ids = reactionToNode[reaction.name]
for gene_id in gene_ids:
for substrate in reaction.substrates:
substrate_id = substrate.name[4:]
if substrate_id in nodes:
importer.add_edge('Edge', substrate_id, gene_id, {'_isNetworkEdge': True})
currentEdges[substrate_id + '_' + gene_id] = {'source': substrate_id, 'target': gene_id}
# create_pathway_edge(edgeDict, substrateNode, node)
if reaction.type == 'reversible':
importer.add_edge('Edge', gene_id, substrate_id, {'_isNetworkEdge': True})
currentEdges[gene_id + '_' + substrate_id] = {'source': gene_id, 'target': substrate_id}
cpdName,
'idType':
'KEGG_COMPOUND',
'url':
'http://www.kegg.jp/dbget-bin/www_bget?cpd:' +
compound_id
})
# node = Node('NETWORK_NODE', 'Compound', id=name, idType='KEGG_COMPOUND', name=name)
# n = batch.create(node)
nodes.add(compound_id)
if compound.id not in compoundDict:
compoundDict[compound.id] = compound_id
currentNodes.add(compound_id)
importer.done_nodes()
for reaction in pathway.reactions:
if reaction.name in reactionToNode:
gene_ids = reactionToNode[reaction.name]
for gene_id in gene_ids:
for substrate in reaction.substrates:
substrate_id = substrate.name[4:]
if substrate_id in nodes:
importer.add_edge('Edge', substrate_id, gene_id,
{'_isNetworkEdge': True})
currentEdges[substrate_id + '_' + gene_id] = {
'source': substrate_id,
'target': gene_id
}
