@@ -8,7 +8,8 @@ import networkx class KeggPathway(networkx.LabeledDiGraph): """ - Represent a Kegg Pathway. Derived from networkx.Digraph + Represent a Kegg Pathway. Derived from networkx.Digraph, it adds: + - reactions: a dictionary of all the reactions in the file >>> p = KeggPathway() >>> p.add_node('gene1', data={'type': 'gene', }) @@ -46,6 +47,7 @@ class KeggPathway(networkx.LabeledDiGraph): """ title = '' labels = {} + reactions = {} def add_node(self, n, data=None): # TODO: in principle, I should redefine all the add_node functions to make sure they contain the right data. networkx.LabeledDiGraph.add_node(self, n, data) @@ -76,6 +78,26 @@ class KeggPathway(networkx.LabeledDiGraph): subgraph.labels = labels return subgraph + def neighbours_labels(self, node): + """ + like networkx.graph.neighbours, but returns gene label + + >>> p = KeggPathway() + + >>> p.add_node(1, data={'label': 'gene1'}) + >>> p.add_node(2, data={'label': 'gene2'}) + >>> p.add_edge(1, 2) + + >>> p.neighbours(1) + [2] + + >>> p.neighbours_labels(1) + 'gene2' + """ + neighbours = self.neighbours(node) + genes = [self.get_node(n)['label' for n in neighbours] + + def __repr__(self): return self.title + ' pathway' # TODO: __init__ method to make sure self.title exists KeggPathway.py 4ef95bedc5a5bbe582346c8c63cc86a9765b8265 dalloliogm dalloliogm@gmail.com http://github.com/dalloliogm/kegg-kgml-parser--python-/commit/a191c632fd4d38601c9d41c7fd8c52e6dccc20b5 a191c632fd4d38601c9d41c7fd8c52e6dccc20b5 2009-10-20T04:04:42-07:00 2009-10-20T04:04:42-07:00 implemented a neighbours_labels method, some refinements 1cd78ebbe76231f8b2b52d3730e2cc9a8107ad91 dalloliogm dalloliogm@gmail.com