biogrid_network.py 文件源码

def main(opts):
    df = pd.read_csv(opts['biogrid'], sep='\t')
    interact_df = df[['Official Symbol Interactor A',
                      'Official Symbol Interactor B']]
    interact_genes = interact_df.dropna().values.tolist()
    G = nx.Graph()
    G.add_edges_from(map(tuple, interact_genes))
    gene_betweeness = nx.betweenness_centrality(G)
    gene_degree = G.degree()

    result = [[key, gene_betweeness[key], gene_degree[key]]
              for key in gene_degree]
    result = [['gene', 'gene_betweeness', 'gene_degree']] + result
    with open(opts['output'], 'wb') as handle:
        csv.writer(handle, delimiter='\t').writerows(result)