def main_library_compile(args): builder = GraphBuilder(args) for path_dir in glob(os.path.join(args.library, "*")): if os.path.isdir(path_dir): path_name = os.path.basename(path_dir) xgmml_path = os.path.join(path_dir, "graph.xgmml") handle = open(xgmml_path) gr = network_convert.read_xgmml(handle) handle.close() fix_gr = builder.fix_graph(gr) spf_path = os.path.join(path_dir, "graph.spf") log("Writing: %s" % (spf_path)) handle = open(spf_path, "w") network_convert.write_spf(fix_gr, handle) handle.close()
def main_library_copy(args): builder = GraphBuilder(args) out_zip = zipfile.ZipFile(args.out, "w") out_base = re.sub( r'.zip$', '', os.path.basename(args.out)) for path_dir in glob(os.path.join(args.library, "*")): if os.path.isdir(path_dir): path_name = os.path.basename(path_dir) xgmml_path = os.path.join(path_dir, "graph.xgmml") handle = open(xgmml_path) gr = network_convert.read_xgmml(handle) handle.close() fix_gr = builder.fix_graph(gr) log("Writing: %s" % (path_name)) text = StringIO() network_convert.write_spf(fix_gr, text) if len(text.getvalue()) > 0: out_zip.writestr( os.path.join(out_base, path_name + ".spf"), text.getvalue()) out_zip.close()
def main_build(args): gr = networkx.MultiDiGraph() paths = pathway_opener( list( (args.pathways[i],args.pathways[i+1]) for i in range(0, len(args.pathways),2) ) ) builer = GraphBuilder(args) type_count = {} interaction_count = {} duplicate_edges = 0 for cur_path in paths: log("Scanning: %s" % (cur_path.name)) cur_gr = cur_path.read() if args.organism is None or cur_gr.graph.get('organism', args.organism) == args.organism: fix_gr = builer.fix_graph(cur_gr) for node in fix_gr.node: if node in gr.node: if 'type' in gr.node[node] and 'type' in fix_gr.node[node] and gr.node[node]['type'] != fix_gr.node[node]['type']: error("%s failure: Mismatch Node Type: %s :%s --> %s" % (cur_path.name, node, gr.node[node]['type'], fix_gr.node[node]['type'] )) if args.rename_nonprotein or args.all: #because 'protein' is a default node type, if we see something not protein, then change the node to match if gr.node[node]['type'] == 'protein': gr.node[node]['type'] = fix_gr.node[node]['type'] else: log("Merging: %s" % node) gr.add_node(node, attr_dict=fix_gr.node[node]) for src, dst, data in fix_gr.edges(data=True): interaction = data['interaction'] src_node_type = fix_gr.node[src].get('type', None) dst_node_type = fix_gr.node[dst].get('type', None) if src in gr.node and dst in gr.node: has_edge = False if dst in gr.edge[src]: for i in gr.edge[src][dst]: if gr.edge[src][dst][i]['interaction'] == interaction: has_edge = True if not has_edge: if not (args.remove_self or args.all) or src != dst: gr.add_edge(src, dst, attr_dict=data ) else: log("Removing self loop: %s" % (src)) else: duplicate_edges += 1 connect_list = networkx.connected_components(networkx.Graph(gr)) rm_list = [] for group in connect_list: if len(group) < args.min_subgraph: rm_list.extend(group) for r in rm_list: gr.remove_node(r) log("+---------------------------+") log("|Node Count: %15d|" % (len(gr.nodes()))) log("|Edge Count: %15d|" % (len(gr.edges()))) log("|Duplicate Edges: %10d|" % (duplicate_edges)) log("|Connected Components: %5d|" % (networkx.number_connected_components(networkx.Graph(gr)))) log("+---------------------------+") if args.output: handle = open(args.output, "w") else: handle = sys.stdout for n_type in type_count: log("Node Type %s: %d" % (n_type, type_count[n_type])) if args.spf: network_convert.write_spf(gr, handle) elif args.sif: network_convert.write_sif(gr, handle) else: network_convert.write_xgmml(gr, handle) handle.close()
z = zipfile.ZipFile(args.cys) for n in z.namelist(): if n.endswith(".xgmml") and os.path.dirname(n).endswith("networks"): handle = z.open(n) gr = convert.read_xgmml(handle) handle.close() """ if gr is not None: if args.out_spf is not None: if args.out_spf == "-": ohandle = sys.stdout else: ohandle = open(args.out_spf, "w") convert.write_spf(gr, ohandle, node_type_field=args.node_type_field, node_type_default=args.node_type_default, edge_type_field=args.edge_type_field, edge_type_default=args.edge_type_default ) if args.out_xgmml is not None: if args.out_xgmml == "-": ohandle = sys.stdout else: ohandle = open(args.out_xgmml, "w") convert.write_xgmml(gr, ohandle) if args.out_gmt: if args.out_gmt == "-": ohandle = sys.stdout else: ohandle = open(args.out_gmt, "w") pathmap = {} for node in gr.node: