Source code for networkx.readwrite.edgelist

"""
**********
Edge Lists
**********
Read and write NetworkX graphs as edge lists.

The multi-line adjacency list format is useful for graphs with nodes
that can be meaningfully represented as strings.  With the edgelist
format simple edge data can be stored but node or graph data is not.
There is no way of representing isolated nodes unless the node has a
self-loop edge.

Format
------
You can read or write three formats of edge lists with these functions.

Node pairs with no data::

 1 2

Python dictionary as data::

 1 2 {'weight':7, 'color':'green'}

Arbitrary data::

 1 2 7 green
"""
__author__ = """Aric Hagberg (hagberg@lanl.gov)\nDan Schult (dschult@colgate.edu)"""
#    Copyright (C) 2004-2019 by
#    Aric Hagberg <hagberg@lanl.gov>
#    Dan Schult <dschult@colgate.edu>
#    Pieter Swart <swart@lanl.gov>
#    All rights reserved.
#    BSD license.

__all__ = ['generate_edgelist',
           'write_edgelist',
           'parse_edgelist',
           'read_edgelist',
           'read_weighted_edgelist',
           'write_weighted_edgelist']

from networkx.utils import open_file, make_str
import networkx as nx


[docs]def generate_edgelist(G, delimiter=' ', data=True): """Generate a single line of the graph G in edge list format. Parameters ---------- G : NetworkX graph delimiter : string, optional Separator for node labels data : bool or list of keys If False generate no edge data. If True use a dictionary representation of edge data. If a list of keys use a list of data values corresponding to the keys. Returns ------- lines : string Lines of data in adjlist format. Examples -------- >>> G = nx.lollipop_graph(4, 3) >>> G[1][2]['weight'] = 3 >>> G[3][4]['capacity'] = 12 >>> for line in nx.generate_edgelist(G, data=False): ... print(line) 0 1 0 2 0 3 1 2 1 3 2 3 3 4 4 5 5 6 >>> for line in nx.generate_edgelist(G): ... print(line) 0 1 {} 0 2 {} 0 3 {} 1 2 {'weight': 3} 1 3 {} 2 3 {} 3 4 {'capacity': 12} 4 5 {} 5 6 {} >>> for line in nx.generate_edgelist(G,data=['weight']): ... print(line) 0 1 0 2 0 3 1 2 3 1 3 2 3 3 4 4 5 5 6 See Also -------- write_adjlist, read_adjlist """ if data is True: for u, v, d in G.edges(data=True): e = u, v, dict(d) yield delimiter.join(map(make_str, e)) elif data is False: for u, v in G.edges(data=False): e = u, v yield delimiter.join(map(make_str, e)) else: for u, v, d in G.edges(data=True): e = [u, v] try: e.extend(d[k] for k in data) except KeyError: pass # missing data for this edge, should warn? yield delimiter.join(map(make_str, e))
[docs]@open_file(1, mode='wb') def write_edgelist(G, path, comments="#", delimiter=' ', data=True, encoding='utf-8'): """Write graph as a list of edges. Parameters ---------- G : graph A NetworkX graph path : file or string File or filename to write. If a file is provided, it must be opened in 'wb' mode. Filenames ending in .gz or .bz2 will be compressed. comments : string, optional The character used to indicate the start of a comment delimiter : string, optional The string used to separate values. The default is whitespace. data : bool or list, optional If False write no edge data. If True write a string representation of the edge data dictionary.. If a list (or other iterable) is provided, write the keys specified in the list. encoding: string, optional Specify which encoding to use when writing file. Examples -------- >>> G=nx.path_graph(4) >>> nx.write_edgelist(G, "test.edgelist") >>> G=nx.path_graph(4) >>> fh=open("test.edgelist",'wb') >>> nx.write_edgelist(G, fh) >>> nx.write_edgelist(G, "test.edgelist.gz") >>> nx.write_edgelist(G, "test.edgelist.gz", data=False) >>> G=nx.Graph() >>> G.add_edge(1,2,weight=7,color='red') >>> nx.write_edgelist(G,'test.edgelist',data=False) >>> nx.write_edgelist(G,'test.edgelist',data=['color']) >>> nx.write_edgelist(G,'test.edgelist',data=['color','weight']) See Also -------- read_edgelist write_weighted_edgelist """ for line in generate_edgelist(G, delimiter, data): line += '\n' path.write(line.encode(encoding))
[docs]def parse_edgelist(lines, comments='#', delimiter=None, create_using=None, nodetype=None, data=True): """Parse lines of an edge list representation of a graph. Parameters ---------- lines : list or iterator of strings Input data in edgelist format comments : string, optional Marker for comment lines delimiter : string, optional Separator for node labels create_using : NetworkX graph constructor, optional (default=nx.Graph) Graph type to create. If graph instance, then cleared before populated. nodetype : Python type, optional Convert nodes to this type. data : bool or list of (label,type) tuples If False generate no edge data or if True use a dictionary representation of edge data or a list tuples specifying dictionary key names and types for edge data. Returns ------- G: NetworkX Graph The graph corresponding to lines Examples -------- Edgelist with no data: >>> lines = ["1 2", ... "2 3", ... "3 4"] >>> G = nx.parse_edgelist(lines, nodetype = int) >>> list(G) [1, 2, 3, 4] >>> list(G.edges()) [(1, 2), (2, 3), (3, 4)] Edgelist with data in Python dictionary representation: >>> lines = ["1 2 {'weight':3}", ... "2 3 {'weight':27}", ... "3 4 {'weight':3.0}"] >>> G = nx.parse_edgelist(lines, nodetype = int) >>> list(G) [1, 2, 3, 4] >>> list(G.edges(data=True)) [(1, 2, {'weight': 3}), (2, 3, {'weight': 27}), (3, 4, {'weight': 3.0})] Edgelist with data in a list: >>> lines = ["1 2 3", ... "2 3 27", ... "3 4 3.0"] >>> G = nx.parse_edgelist(lines, nodetype = int, data=(('weight',float),)) >>> list(G) [1, 2, 3, 4] >>> list(G.edges(data=True)) [(1, 2, {'weight': 3.0}), (2, 3, {'weight': 27.0}), (3, 4, {'weight': 3.0})] See Also -------- read_weighted_edgelist """ from ast import literal_eval G = nx.empty_graph(0, create_using) for line in lines: p = line.find(comments) if p >= 0: line = line[:p] if not len(line): continue # split line, should have 2 or more s = line.strip().split(delimiter) if len(s) < 2: continue u = s.pop(0) v = s.pop(0) d = s if nodetype is not None: try: u = nodetype(u) v = nodetype(v) except: raise TypeError("Failed to convert nodes %s,%s to type %s." % (u, v, nodetype)) if len(d) == 0 or data is False: # no data or data type specified edgedata = {} elif data is True: # no edge types specified try: # try to evaluate as dictionary edgedata = dict(literal_eval(' '.join(d))) except: raise TypeError( "Failed to convert edge data (%s) to dictionary." % (d)) else: # convert edge data to dictionary with specified keys and type if len(d) != len(data): raise IndexError( "Edge data %s and data_keys %s are not the same length" % (d, data)) edgedata = {} for (edge_key, edge_type), edge_value in zip(data, d): try: edge_value = edge_type(edge_value) except: raise TypeError( "Failed to convert %s data %s to type %s." % (edge_key, edge_value, edge_type)) edgedata.update({edge_key: edge_value}) G.add_edge(u, v, **edgedata) return G
[docs]@open_file(0, mode='rb') def read_edgelist(path, comments="#", delimiter=None, create_using=None, nodetype=None, data=True, edgetype=None, encoding='utf-8'): """Read a graph from a list of edges. Parameters ---------- path : file or string File or filename to read. If a file is provided, it must be opened in 'rb' mode. Filenames ending in .gz or .bz2 will be uncompressed. comments : string, optional The character used to indicate the start of a comment. delimiter : string, optional The string used to separate values. The default is whitespace. create_using : NetworkX graph constructor, optional (default=nx.Graph) Graph type to create. If graph instance, then cleared before populated. nodetype : int, float, str, Python type, optional Convert node data from strings to specified type data : bool or list of (label,type) tuples Tuples specifying dictionary key names and types for edge data edgetype : int, float, str, Python type, optional OBSOLETE Convert edge data from strings to specified type and use as 'weight' encoding: string, optional Specify which encoding to use when reading file. Returns ------- G : graph A networkx Graph or other type specified with create_using Examples -------- >>> nx.write_edgelist(nx.path_graph(4), "test.edgelist") >>> G=nx.read_edgelist("test.edgelist") >>> fh=open("test.edgelist", 'rb') >>> G=nx.read_edgelist(fh) >>> fh.close() >>> G=nx.read_edgelist("test.edgelist", nodetype=int) >>> G=nx.read_edgelist("test.edgelist",create_using=nx.DiGraph) Edgelist with data in a list: >>> textline = '1 2 3' >>> fh = open('test.edgelist','w') >>> d = fh.write(textline) >>> fh.close() >>> G = nx.read_edgelist('test.edgelist', nodetype=int, data=(('weight',float),)) >>> list(G) [1, 2] >>> list(G.edges(data=True)) [(1, 2, {'weight': 3.0})] See parse_edgelist() for more examples of formatting. See Also -------- parse_edgelist write_edgelist Notes ----- Since nodes must be hashable, the function nodetype must return hashable types (e.g. int, float, str, frozenset - or tuples of those, etc.) """ lines = (line if isinstance(line, str) else line.decode(encoding) for line in path) return parse_edgelist(lines, comments=comments, delimiter=delimiter, create_using=create_using, nodetype=nodetype, data=data)
[docs]def write_weighted_edgelist(G, path, comments="#", delimiter=' ', encoding='utf-8'): """Write graph G as a list of edges with numeric weights. Parameters ---------- G : graph A NetworkX graph path : file or string File or filename to write. If a file is provided, it must be opened in 'wb' mode. Filenames ending in .gz or .bz2 will be compressed. comments : string, optional The character used to indicate the start of a comment delimiter : string, optional The string used to separate values. The default is whitespace. encoding: string, optional Specify which encoding to use when writing file. Examples -------- >>> G=nx.Graph() >>> G.add_edge(1,2,weight=7) >>> nx.write_weighted_edgelist(G, 'test.weighted.edgelist') See Also -------- read_edgelist write_edgelist read_weighted_edgelist """ write_edgelist(G, path, comments=comments, delimiter=delimiter, data=('weight',), encoding=encoding)
[docs]def read_weighted_edgelist(path, comments="#", delimiter=None, create_using=None, nodetype=None, encoding='utf-8'): """Read a graph as list of edges with numeric weights. Parameters ---------- path : file or string File or filename to read. If a file is provided, it must be opened in 'rb' mode. Filenames ending in .gz or .bz2 will be uncompressed. comments : string, optional The character used to indicate the start of a comment. delimiter : string, optional The string used to separate values. The default is whitespace. create_using : NetworkX graph constructor, optional (default=nx.Graph) Graph type to create. If graph instance, then cleared before populated. nodetype : int, float, str, Python type, optional Convert node data from strings to specified type encoding: string, optional Specify which encoding to use when reading file. Returns ------- G : graph A networkx Graph or other type specified with create_using Notes ----- Since nodes must be hashable, the function nodetype must return hashable types (e.g. int, float, str, frozenset - or tuples of those, etc.) Example edgelist file format. With numeric edge data:: # read with # >>> G=nx.read_weighted_edgelist(fh) # source target data a b 1 a c 3.14159 d e 42 See Also -------- write_weighted_edgelist """ return read_edgelist(path, comments=comments, delimiter=delimiter, create_using=create_using, nodetype=nodetype, data=(('weight', float),), encoding=encoding )
# fixture for pytest def teardown_module(module): import os for fname in ['test.edgelist', 'test.edgelist.gz', 'test.weighted.edgelist']: if os.path.isfile(fname): os.unlink(fname)