"""
**********
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) 2004-2015 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 or data is False:
for e in G.edges(data=data):
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
--------
write_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 container, optional
Use given NetworkX graph for holding nodes or edges.
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)
>>> G.nodes()
[1, 2, 3, 4]
>>> 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)
>>> G.nodes()
[1, 2, 3, 4]
>>> 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),))
>>> G.nodes()
[1, 2, 3, 4]
>>> 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
if create_using is None:
G=nx.Graph()
else:
try:
G=create_using
G.clear()
except:
raise TypeError("create_using input is not a NetworkX graph type")
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, attr_dict=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 : Graph container, optional,
Use specified container to build graph. The default is networkx.Graph,
an undirected graph.
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),))
>>> G.nodes()
[1, 2]
>>> G.edges(data = True)
[(1, 2, {'weight': 3.0})]
See parse_edgelist() for more examples of formatting.
See Also
--------
parse_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.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()
write_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 : Graph container, optional,
Use specified container to build graph. The default is networkx.Graph,
an undirected graph.
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
"""
return read_edgelist(path,
comments=comments,
delimiter=delimiter,
create_using=create_using,
nodetype=nodetype,
data=(('weight',float),),
encoding = encoding
)
# fixture for nose tests
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)