@@ -24,24 +24,35 @@ class KeggPathway(networkx.LabeledDiGraph): To get a list of the nodes, use the .nodes() method >>> graph.nodes()[0:5] - ['ALG8', 'ALG9', 'GCS1', 'ST6GAL1', 'ALG2'] + ['56', '54', '42', '48', '43'] >>> len(graph.nodes()) - 72 + 76 + >>> print [graph.get_node(n)['label'] for n in graph.nodes()][0:5] + ['MGAT1', 'MGAT2', 'C01246', 'TITLE:N-Glycan biosynthesis', 'C03862'] + >>> graph.edges()[0:5] - [('ALG8', 'ALG6'), ('ALG9', 'ALG3'), ('GCS1', 'DAD1'), ('ST6GAL1', 'Other glycan degradation'), ('ALG2', 'ALG1')] + [('56', '57'), ('54', '55'), ('54', '37'), ('54', '58'), ('60', '62')] To get detailed informations on a node, use .get_node: - >>> graph.get_node('ALG8') - {'xy': (400, 408), 'type': 'gene'} + >>> graph.get_node('10') + {'xy': (580, 317), 'type': 'gene', 'label': 'ALG12'} All the annotations (such as node type, etc..), are stored in the .label attribute - >>> graph.label['ALG8'] #doctest: +ELLIPSIS - {'xy': (400, 408), 'type': 'gene'} + >>> graph.label['10'] #doctest: +ELLIPSIS + {'xy': (580, 317), 'type': 'gene', 'label': 'ALG12'} To obtain a subgraph with only the genes of the pathway, it is recommended to use get_genes: >>> genes_graph = graph.get_genes() >>> genes_graph.edges()[0:4] - [('ALG8', 'ALG6'), ('ALG9', 'ALG3'), ('GCS1', 'DAD1'), ('ALG2', 'ALG1')] + [('60', '62'), ('63', '3'), ('63', '2'), ('63', '72')] + + >>> for (node1, node2) in genes_graph.edges()[0:4]: + ... print genes_graph.get_node(node1)['label'], genes_graph.get_node(node2)['label'] + GCS1 DAD1... + ALG5 DPM2 + ALG5 DPM3 + ALG5 DPAGT1 + """ @@ -70,7 +81,7 @@ class KeggPathway(networkx.LabeledDiGraph): for node in self.nodes(): if self.get_node(node)['type'] == 'gene': genes.append(node) - labels[node] = self.labels[node] + labels[node] = self.get_node(node) # else: # self.labels.pop(node) subgraph = self.subgraph(genes) @@ -88,11 +99,11 @@ class KeggPathway(networkx.LabeledDiGraph): >>> p.add_node(2, data={'label': 'gene2'}) >>> p.add_edge(1, 2) - >>> p.neighbours(1) + >>> p.neighbors(1) [2] >>> p.neighbors_labels(1) - 'gene2' + {'gene1': ['gene2']} """ neighbours = self.neighbors(node) labels = [self.get_node(n)['label'] for n in neighbours] KeggPathway.py 977f3c1218d05e97ce0c1b9ff57155e8cca42c80 dalloliogm dalloliogm@gmail.com http://github.com/dalloliogm/kegg-kgml-parser--python-/commit/0e9feb7d8e16941ac1fee4426b2aae18040e7d61 0e9feb7d8e16941ac1fee4426b2aae18040e7d61 2009-10-20T04:27:09-07:00 2009-10-20T04:27:09-07:00 fixed doctests, not sure why the number of nodes ahas changed be809a2bcb66cffceb538e422268548304fa295c dalloliogm dalloliogm@gmail.com