def write_adjlist(G, path, comments="#", delimiter=' '):
"""Write graph G in single-line adjacency-list format to path.
See read_adjlist for file format details.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_adjlist(G,"test.adjlist")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.adjlist",'w')
>>> nx.write_adjlist(G, fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_adjlist(G, "test.adjlist.gz")
The file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
fh=codecs.open("test.adjlist",encoding='utf=8') # use utf-8 encoding
nx.write_adjlist(G,fh)
Does not handle edge data.
Use 'write_edgelist' or 'write_multiline_adjlist'
"""
fh = _get_fh(path, mode='w')
pargs = comments + " " + string.join(sys.argv, ' ')
fh.write("%s\n" % (pargs))
fh.write(comments + " GMT %s\n" % (time.asctime(time.gmtime())))
fh.write(comments + " %s\n" % (G.name))
def make_str(t):
if is_string_like(t): return t
return str(t)
directed = G.directed
seen = {}
for s, nbrs in G.adjacency_iter():
fh.write(make_str(s) + delimiter)
for t, data in nbrs.iteritems():
if not directed and t in seen: continue
if G.multigraph:
for d in data:
fh.write(make_str(t) + delimiter)
else:
fh.write(make_str(t) + delimiter)
fh.write("\n")
if not directed:
seen[s] = 1
def write_adjlist(G, path, comments="#", delimiter=' '):
"""Write graph G in single-line adjacency-list format to path.
See read_adjlist for file format details.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_adjlist(G,"test.adjlist")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.adjlist",'w')
>>> nx.write_adjlist(G, fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_adjlist(G, "test.adjlist.gz")
The file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
fh=codecs.open("test.adjlist",encoding='utf=8') # use utf-8 encoding
nx.write_adjlist(G,fh)
Does not handle edge data.
Use 'write_edgelist' or 'write_multiline_adjlist'
"""
fh=_get_fh(path,mode='w')
pargs=comments+" "+string.join(sys.argv,' ')
fh.write("%s\n" % (pargs))
fh.write(comments+" GMT %s\n" % (time.asctime(time.gmtime())))
fh.write(comments+" %s\n" % (G.name))
def make_str(t):
if is_string_like(t): return t
return str(t)
directed=G.directed
seen={}
for s,nbrs in G.adjacency_iter():
fh.write(make_str(s)+delimiter)
for t,data in nbrs.iteritems():
if not directed and t in seen: continue
if G.multigraph:
for d in data:
fh.write(make_str(t)+delimiter)
else:
fh.write(make_str(t)+delimiter)
fh.write("\n")
if not directed:
seen[s]=1
def write_edgelist(G, path, comments="#", delimiter=' '):
"""Write graph as a list of edges.
Parameters
----------
G : graph
A networkx_v099 graph
path : file or string
File or filename to write.
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 uses to separate values. The default is whitespace.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_edgelist(G, "test.edgelist")
>>> fh=open("test.edgelist",'w')
>>> nx.write_edgelist(G,fh)
>>> nx.write_edgelist(G, "test.edgelist.gz")
Notes
-----
The file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
>>> fh=codecs.open("test.edgelist",'w',encoding='utf=8') # utf-8 encoding
>>> nx.write_edgelist(G,fh)
See Also
--------
networkx_v099.write_edgelist
"""
fh=_get_fh(path,mode='w')
pargs=comments+" "+string.join(sys.argv,' ')
fh.write("%s\n" % (pargs))
fh.write(comments+" GMT %s\n" % (time.asctime(time.gmtime())))
fh.write(comments+" %s\n" % (G.name))
def make_str(t):
if is_string_like(t): return t
return str(t)
for e in G.edges(data=True):
fh.write(delimiter.join(map(make_str,e))+"\n")
def write_edgelist(G, path, comments="#", delimiter=' '):
"""Write graph as a list of edges.
Parameters
----------
G : graph
A networkx_v099 graph
path : file or string
File or filename to write.
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 uses to separate values. The default is whitespace.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_edgelist(G, "test.edgelist")
>>> fh=open("test.edgelist",'w')
>>> nx.write_edgelist(G,fh)
>>> nx.write_edgelist(G, "test.edgelist.gz")
Notes
-----
The file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
>>> fh=codecs.open("test.edgelist",'w',encoding='utf=8') # utf-8 encoding
>>> nx.write_edgelist(G,fh)
See Also
--------
networkx_v099.write_edgelist
"""
fh = _get_fh(path, mode='w')
pargs = comments + " " + string.join(sys.argv, ' ')
fh.write("%s\n" % (pargs))
fh.write(comments + " GMT %s\n" % (time.asctime(time.gmtime())))
fh.write(comments + " %s\n" % (G.name))
def make_str(t):
if is_string_like(t): return t
return str(t)
for e in G.edges(data=True):
fh.write(delimiter.join(map(make_str, e)) + "\n")
def read_p2g(path):
"""Read graph in p2g format from path. Returns an XDiGraph.
If you want a DiGraph (with no self loops allowed and no edge data)
use D=networkx_v099.DiGraph(read_p2g(path))
"""
fh=_get_fh(path,mode='r')
G=parse_p2g(fh)
return G
def read_p2g(path):
"""Read graph in p2g format from path. Returns an XDiGraph.
If you want a DiGraph (with no self loops allowed and no edge data)
use D=networkx_v099.DiGraph(read_p2g(path))
"""
fh = _get_fh(path, mode='r')
G = parse_p2g(fh)
return G
def read_sparse6_list(path):
"""Read simple undirected graphs in sparse6 format from path.
Returns a list of Graphs, one for each line in file."""
fh=_get_fh(path,mode='r')
glist=[]
for line in fh:
line = line.strip()
if not len(line): continue
glist.append(parse_sparse6(line))
return glist
def read_sparse6_list(path):
"""Read simple undirected graphs in sparse6 format from path.
Returns a list of Graphs, one for each line in file."""
fh = _get_fh(path, mode='r')
glist = []
for line in fh:
line = line.strip()
if not len(line): continue
glist.append(parse_sparse6(line))
return glist
def write_dot(G,path):
"""Write Networkx_v099 graph G to Graphviz dot format on path.
Path can be a string or a file handle.
"""
fh=_get_fh(path,'w')
P=to_pydot(G)
fh.write(P.to_string())
fh.flush() # might be a user filehandle so leave open (but flush)
return
def read_dot(path):
"""Return a Networkx_v099 Graph or DiGraph from a dot file on path.
Path can be a string or a file handle.
"""
fh=_get_fh(path,'r')
data=fh.read()
P=pydot.graph_from_dot_data(data)
return from_pydot(P)
def write_dot(G, path):
"""Write Networkx_v099 graph G to Graphviz dot format on path.
Path can be a string or a file handle.
"""
fh = _get_fh(path, 'w')
P = to_pydot(G)
fh.write(P.to_string())
fh.flush() # might be a user filehandle so leave open (but flush)
return
def read_dot(path):
"""Return a Networkx_v099 Graph or DiGraph from a dot file on path.
Path can be a string or a file handle.
"""
fh = _get_fh(path, 'r')
data = fh.read()
P = pydot.graph_from_dot_data(data)
return from_pydot(P)
def read_gml(path):
"""Read graph in GML format from path.
Returns an Graph or DiGraph.
This doesn't implement the complete GML specification for
nested attributes for graphs, edges, and nodes.
"""
fh = _get_fh(path, mode='r')
G = parse_gml(fh)
return G
def read_gml(path):
"""Read graph in GML format from path.
Returns an Graph or DiGraph.
This doesn't implement the complete GML specification for
nested attributes for graphs, edges, and nodes.
"""
fh=_get_fh(path,mode='r')
G=parse_gml(fh)
return G
def write_yaml(G, path, default_flow_style=False, **kwds):
"""Write graph G in YAML text format to path.
See http://www.yaml.org
"""
try:
import yaml
except ImportError:
raise ImportError, \
"Import Error: not able to import yaml: http://www.yaml.org "
fh=_get_fh(path,mode='w')
yaml.dump(G,fh,default_flow_style=default_flow_style,**kwds)
def write_yaml(G, path, default_flow_style=False, **kwds):
"""Write graph G in YAML text format to path.
See http://www.yaml.org
"""
try:
import yaml
except ImportError:
raise ImportError, \
"Import Error: not able to import yaml: http://www.yaml.org "
fh = _get_fh(path, mode='w')
yaml.dump(G, fh, default_flow_style=default_flow_style, **kwds)
def write_pajek(G, path):
"""Write Networkx_v099 graph in pajek format to path.
"""
fh=_get_fh(path,mode='w')
fh.write("*network %s\n"%G.name)
# write nodes with attributes
fh.write("*vertices %s\n"%(G.order()))
nodes = G.nodes()
# make dictionary mapping nodes to integers
nodenumber=dict(zip(nodes,range(1,len(nodes)+1)))
try:
node_attr=G.node_attr
except:
node_attr={}
for n in nodes:
na=node_attr.get(n,{})
x=na.pop('x',0.0)
y=na.pop('y',0.0)
id=int(na.pop('id',nodenumber[n]))
nodenumber[n]=id
shape=na.pop('shape','ellipse')
fh.write("%d \"%s\" %f %f %s "%(id,n,float(x),float(y),shape))
for k,v in na.items():
fh.write("%s %s "%(k,v))
fh.write("\n")
# write edges with attributes
if G.is_directed():
fh.write("*arcs\n")
else:
fh.write("*edges\n")
for e in G.edges():
if len(e)==3:
u,v,d=e
if type(d)!=type({}):
if d is None:
d=1.0
d={'value':float(d)}
else:
u,v=e
d={}
value=d.pop('value',1.0) # use 1 as default edge value
fh.write("%d %d %f "%(nodenumber[u],nodenumber[v],float(value)))
for k,v in d.items():
if " " in v: # add quotes to any values with a blank space
v="\"%s\""%v
fh.write("%s %s "%(k,v))
fh.write("\n")
fh.close()
def write_pajek(G, path):
"""Write Networkx_v099 graph in pajek format to path.
"""
fh = _get_fh(path, mode='w')
fh.write("*network %s\n" % G.name)
# write nodes with attributes
fh.write("*vertices %s\n" % (G.order()))
nodes = G.nodes()
# make dictionary mapping nodes to integers
nodenumber = dict(zip(nodes, range(1, len(nodes) + 1)))
try:
node_attr = G.node_attr
except:
node_attr = {}
for n in nodes:
na = node_attr.get(n, {})
x = na.pop('x', 0.0)
y = na.pop('y', 0.0)
id = int(na.pop('id', nodenumber[n]))
nodenumber[n] = id
shape = na.pop('shape', 'ellipse')
fh.write("%d \"%s\" %f %f %s " % (id, n, float(x), float(y), shape))
for k, v in na.items():
fh.write("%s %s " % (k, v))
fh.write("\n")
# write edges with attributes
if G.is_directed():
fh.write("*arcs\n")
else:
fh.write("*edges\n")
for e in G.edges():
if len(e) == 3:
u, v, d = e
if type(d) != type({}):
if d is None:
d = 1.0
d = {'value': float(d)}
else:
u, v = e
d = {}
value = d.pop('value', 1.0) # use 1 as default edge value
fh.write("%d %d %f " % (nodenumber[u], nodenumber[v], float(value)))
for k, v in d.items():
if " " in v: # add quotes to any values with a blank space
v = "\"%s\"" % v
fh.write("%s %s " % (k, v))
fh.write("\n")
fh.close()
def read_gpickle(path):
"""
Read graph object in Python pickle format
G=nx.path_graph(4)
nx.write_gpickle(G,"test.gpickle")
G=nx.read_gpickle("test.gpickle")
See cPickle.
"""
fh = _get_fh(path, 'rb')
return pickle.load(fh)
def read_yaml(path):
"""Read graph from YAML format from path.
See http://www.yaml.org
"""
try:
import yaml
except ImportError:
raise ImportError, \
"Import Error: not able to import yaml: http://www.yaml.org "
fh=_get_fh(path,mode='r')
return yaml.load(fh)
def read_yaml(path):
"""Read graph from YAML format from path.
See http://www.yaml.org
"""
try:
import yaml
except ImportError:
raise ImportError, \
"Import Error: not able to import yaml: http://www.yaml.org "
fh = _get_fh(path, mode='r')
return yaml.load(fh)
def write_gpickle(G, path):
"""
Write graph object in Python pickle format.
This will preserve Python objects used as nodes or edges.
>>> G=nx.path_graph(4)
>>> nx.write_gpickle(G,"test.gpickle")
See cPickle.
"""
fh = _get_fh(path, mode='wb')
pickle.dump(G, fh, pickle.HIGHEST_PROTOCOL)
def read_gpickle(path):
"""
Read graph object in Python pickle format
G=nx.path_graph(4)
nx.write_gpickle(G,"test.gpickle")
G=nx.read_gpickle("test.gpickle")
See cPickle.
"""
fh=_get_fh(path,'rb')
return pickle.load(fh)
def write_gpickle(G, path):
"""
Write graph object in Python pickle format.
This will preserve Python objects used as nodes or edges.
>>> G=nx.path_graph(4)
>>> nx.write_gpickle(G,"test.gpickle")
See cPickle.
"""
fh=_get_fh(path,mode='wb')
pickle.dump(G,fh,pickle.HIGHEST_PROTOCOL)
def write_p2g(G, path):
"""Write Networkx_v099 graph in p2g format.
This format is meant to be used with directed graphs with
possible self loops.
"""
fh=_get_fh(path,mode='w')
fh.write("%s\n"%G.name)
fh.write("%s %s\n"%(G.order(),G.size()))
nodes = G.nodes()
# make dictionary mapping nodes to integers
nodenumber=dict(zip(nodes,range(len(nodes))))
for n in nodes:
fh.write("%s\n"%n)
for nbr in G.neighbors(n):
fh.write("%s "%nodenumber[nbr])
fh.write("\n")
fh.close()
def write_p2g(G, path):
"""Write Networkx_v099 graph in p2g format.
This format is meant to be used with directed graphs with
possible self loops.
"""
fh = _get_fh(path, mode='w')
fh.write("%s\n" % G.name)
fh.write("%s %s\n" % (G.order(), G.size()))
nodes = G.nodes()
# make dictionary mapping nodes to integers
nodenumber = dict(zip(nodes, range(len(nodes))))
for n in nodes:
fh.write("%s\n" % n)
for nbr in G.neighbors(n):
fh.write("%s " % nodenumber[nbr])
fh.write("\n")
fh.close()
def read_edgelist(path,
comments="#",
delimiter=' ',
create_using=None,
nodetype=None,
edgetype=None):
"""Read a graph from a list of edges.
Parameters
----------
path : file or string
File or filename to write.
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 uses to separate values. The default is whitespace.
create_using : Graph container, optional
Use specified Graph container to build graph. The default is
nx.Graph().
nodetype : int, float, str, Python type, optional
Convert node data from strings to specified type
edgetype : int, float, str, Python type, optional
Convert edge data from strings to specified type
Returns
----------
out : graph
A networkx_v099 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")
>>> G=nx.read_edgelist(fh)
>>> G=nx.read_edgelist("test.edgelist", nodetype=int)
>>> G=nx.read_edgelist("test.edgelist",create_using=nx.DiGraph())
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 formats
Without edge data::
# source target
a b
a c
d e
With edge data:::
# source target data
a b 1
a c 3.14159
d e apple
"""
if create_using is None:
G = networkx_v099.Graph()
else:
try:
G = create_using
G.clear()
except:
raise TypeError("Input graph is not a networkx_v099 graph type")
fh = _get_fh(path)
for line in fh.readlines():
line = line[:line.find(comments)].strip()
if not len(line): continue
# if line.startswith("#") or line.startswith("\n"):
# continue
# line=line.strip() #remove trailing \n
# split line, should have 2 or three items
s = line.split(delimiter)
if len(s) == 2:
if nodetype is not None:
try:
(u, v) = map(nodetype, s)
except:
raise TypeError("Failed to convert edge %s to type %s"\
%(s,nodetype))
else:
(u, v) = s
G.add_edge(u, v)
elif len(s) == 3:
(u, v, d) = s
if nodetype is not None:
try:
(u, v) = map(nodetype, (u, v))
except:
raise TypeError("Failed to convert edge (%s, %s) to type %s"\
%(u,v,nodetype))
if d is not None and edgetype is not None:
try:
d = edgetype(d)
except:
raise TypeError("Failed to convert edge data (%s) to type %s"\
%(d, edgetype))
G.add_edge(u, v, d) # XGraph or XDiGraph
else:
raise TypeError("Failed to read line: %s" % line)
return G
def write_gml(G, path):
"""
Write the graph G in GML format to the file or file handle path.
Examples
---------
>>> G=nx.path_graph(4)
>>> nx.write_gml(G,"test.gml")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.gml",'w')
>>> nx.write_gml(G,fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_gml(G,"test.gml.gz")
The output file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
>>> fh=codecs.open("test.gml",'w',encoding='iso8859-1')# use iso8859-1
>>> nx.write_gml(G,fh)
GML specifications indicate that the file should only use
7bit ASCII text encoding.iso8859-1 (latin-1).
Only a single level of attributes for graphs, nodes, and edges,
is supported.
"""
fh=_get_fh(path,mode='w')
# comments="#"
# pargs=comments+" "+' '.join(sys.argv)
# fh.write("%s\n" % (pargs))
# fh.write(comments+" GMT %s\n" % (time.asctime(time.gmtime())))
# fh.write(comments+" %s\n" % (G.name))
# check for attributes or assign empty dict
if hasattr(G,'graph_attr'):
graph_attr=G.graph_attr
else:
graph_attr={}
if hasattr(G,'node_attr'):
node_attr=G.node_attr
else:
node_attr={}
indent=2*' '
count=iter(range(G.number_of_nodes()))
node_id={}
fh.write("graph [\n")
# write graph attributes
for k,v in graph_attr.items():
if is_string_like(v):
v='"'+v+'"'
fh.write(indent+"%s %s\n"%(k,v))
# write nodes
for n in G:
fh.write(indent+"node [\n")
# get id or assign number
if n in node_attr:
nid=node_attr[n].get('id',count.next())
else:
nid=count.next()
node_id[n]=nid
fh.write(2*indent+"id %s\n"%nid)
fh.write(2*indent+"label \"%s\"\n"%n)
if n in node_attr:
for k,v in node_attr[n].items():
if is_string_like(v): v='"'+v+'"'
if k=='id': continue
fh.write(2*indent+"%s %s\n"%(k,v))
fh.write(indent+"]\n")
# write edges
for e in G.edges_iter():
if len(e)==3:
u,v,d=e
# try to guess what is on the edge and do something reasonable
edgedata={}
if d is None: # no data
pass
elif hasattr(d,'iteritems'): # try dict-like
edgedata=dict(d.iteritems())
elif hasattr(d,'__iter__'): # some kind of container
edgedata['data']=d.__repr__()
else: # something else - string, number
edgedata['data']=d
else:
u,v=e
edgedata={}
fh.write(indent+"edge [\n")
fh.write(2*indent+"source %s\n"%node_id[u])
fh.write(2*indent+"target %s\n"%node_id[v])
for k,v in edgedata.items():
if k=='source': continue
if k=='target': continue
if is_string_like(v): v='"'+v+'"'
fh.write(2*indent+"%s %s\n"%(k,v))
fh.write(indent+"]\n")
fh.write("]\n")
def read_graphml(path):
"""Read graph in GraphML format from path.
Returns an Graph or DiGraph."""
fh = _get_fh(path, mode='r')
G = parse_graphml(fh)
return G
def read_graphml(path):
"""Read graph in GraphML format from path.
Returns an Graph or DiGraph."""
fh=_get_fh(path,mode='r')
G=parse_graphml(fh)
return G
def read_adjlist(path,
comments="#",
delimiter=' ',
create_using=None,
nodetype=None):
"""Read graph in single line adjacency list format from path.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_adjlist(G, "test.adjlist")
>>> G=nx.read_adjlist("test.adjlist")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.adjlist")
>>> G=nx.read_adjlist(fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_adjlist(G, "test.adjlist.gz")
>>> G=nx.read_adjlist("test.adjlist.gz")
nodetype is an optional function to convert node strings to nodetype
For example
>>> G=nx.read_adjlist("test.adjlist", nodetype=int)
will attempt to convert all nodes to integer type
Since nodes must be hashable, the function nodetype must return hashable
types (e.g. int, float, str, frozenset - or tuples of those, etc.)
create_using is an optional networkx_v099 graph type, the default is
Graph(), an undirected graph.
>>> G=nx.read_adjlist("test.adjlist", create_using=nx.DiGraph())
Does not handle edge data: use 'read_edgelist' or 'read_multiline_adjlist'
The comments character (default='#') at the beginning of a
line indicates a comment line.
The entries are separated by delimiter (default=' ').
If whitespace is significant in node or edge labels you should use
some other delimiter such as a tab or other symbol.
Sample format::
# source target
a b c
d e
"""
if create_using is None:
G = networkx_v099.Graph()
else:
try:
G = create_using
G.clear()
except:
raise TypeError("Input graph is not a networkx_v099 graph type")
fh = _get_fh(path)
for line in fh.readlines():
line = line[:line.find(comments)].strip()
if not len(line): continue
# if line.startswith("#") or line.startswith("\n"):
# continue
# line=line.strip() #remove trailing \n
vlist = line.split(delimiter)
u = vlist.pop(0)
# convert types
if nodetype is not None:
try:
u = nodetype(u)
except:
raise TypeError("Failed to convert node (%s) to type %s"\
%(u,nodetype))
G.add_node(u)
try:
vlist = map(nodetype, vlist)
except:
raise TypeError("Failed to convert nodes (%s) to type %s"\
%(','.join(vlist),nodetype))
for v in vlist:
G.add_edge(u, v)
return G
def read_adjlist(path, comments="#", delimiter=' ',
create_using=None, nodetype=None):
"""Read graph in single line adjacency list format from path.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_adjlist(G, "test.adjlist")
>>> G=nx.read_adjlist("test.adjlist")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.adjlist")
>>> G=nx.read_adjlist(fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_adjlist(G, "test.adjlist.gz")
>>> G=nx.read_adjlist("test.adjlist.gz")
nodetype is an optional function to convert node strings to nodetype
For example
>>> G=nx.read_adjlist("test.adjlist", nodetype=int)
will attempt to convert all nodes to integer type
Since nodes must be hashable, the function nodetype must return hashable
types (e.g. int, float, str, frozenset - or tuples of those, etc.)
create_using is an optional networkx_v099 graph type, the default is
Graph(), an undirected graph.
>>> G=nx.read_adjlist("test.adjlist", create_using=nx.DiGraph())
Does not handle edge data: use 'read_edgelist' or 'read_multiline_adjlist'
The comments character (default='#') at the beginning of a
line indicates a comment line.
The entries are separated by delimiter (default=' ').
If whitespace is significant in node or edge labels you should use
some other delimiter such as a tab or other symbol.
Sample format::
# source target
a b c
d e
"""
if create_using is None:
G=networkx_v099.Graph()
else:
try:
G=create_using
G.clear()
except:
raise TypeError("Input graph is not a networkx_v099 graph type")
fh=_get_fh(path)
for line in fh.readlines():
line = line[:line.find(comments)].strip()
if not len(line): continue
# if line.startswith("#") or line.startswith("\n"):
# continue
# line=line.strip() #remove trailing \n
vlist=line.split(delimiter)
u=vlist.pop(0)
# convert types
if nodetype is not None:
try:
u=nodetype(u)
except:
raise TypeError("Failed to convert node (%s) to type %s"\
%(u,nodetype))
G.add_node(u)
try:
vlist=map(nodetype,vlist)
except:
raise TypeError("Failed to convert nodes (%s) to type %s"\
%(','.join(vlist),nodetype))
for v in vlist:
G.add_edge(u,v)
return G
def read_pajek(path):
"""Read graph in pajek format from path. Returns an XGraph or XDiGraph.
"""
fh=_get_fh(path,mode='r')
G=parse_pajek(fh)
return G
def write_multiline_adjlist(G, path, delimiter=' ', comments='#'):
"""
Write the graph G in multiline adjacency list format to the file
or file handle path.
See read_multiline_adjlist for file format details.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_multiline_adjlist(G,"test.adjlist")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.adjlist",'w')
>>> nx.write_multiline_adjlist(G,fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_multiline_adjlist(G,"test.adjlist.gz")
The file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
>>> fh=codecs.open("test.adjlist",'w',encoding='utf=8') # utf-8 encoding
>>> nx.write_multiline_adjlist(G,fh)
"""
fh=_get_fh(path,mode='w')
pargs=comments+" "+string.join(sys.argv,' ')
fh.write("%s\n" % (pargs))
fh.write(comments+" GMT %s\n" % (time.asctime(time.gmtime())))
fh.write(comments+" %s\n" % (G.name))
def make_str(t):
if is_string_like(t): return t
return str(t)
if G.directed:
if G.multigraph:
for s,nbrs in G.adjacency_iter():
nbr_edges=[ (u,d) for u,dl in nbrs.iteritems() for d in dl]
deg=len(nbr_edges)
fh.write(make_str(s)+delimiter+"%i\n"%(deg))
for u,d in nbr_edges:
if d is None:
fh.write(make_str(u)+'\n')
else:
fh.write(make_str(u)+delimiter+make_str(d)+"\n")
else: # directed single edges
for s,nbrs in G.adjacency_iter():
deg=len(nbrs)
fh.write(make_str(s)+delimiter+"%i\n"%(deg))
for u,d in nbrs.iteritems():
if d is None:
fh.write(make_str(u)+'\n')
else:
fh.write(make_str(u)+delimiter+make_str(d)+"\n")
else: #undirected
if G.multigraph:
seen={} # helper dict used to avoid duplicate edges
for s,nbrs in G.adjacency_iter():
nbr_edges=[ (u,d) for u,dl in nbrs.iteritems() if u not in seen for d in dl]
deg=len(nbr_edges)
fh.write(make_str(s)+delimiter+"%i\n"%(deg))
for u,d in nbr_edges:
if d is None:
fh.write(make_str(u)+'\n')
else:
fh.write(make_str(u)+delimiter+make_str(d)+"\n")
seen[s]=1
else: # undirected single edges
seen={} # helper dict used to avoid duplicate edges
for s,nbrs in G.adjacency_iter():
nbr_edges=[ (u,d) for u,d in nbrs.iteritems() if u not in seen]
deg=len(nbr_edges)
fh.write(make_str(s)+delimiter+"%i\n"%(deg))
for u,d in nbr_edges:
if d is None:
fh.write(make_str(u)+'\n')
else:
fh.write(make_str(u)+delimiter+make_str(d)+"\n")
seen[s]=1
def read_multiline_adjlist(path,
comments="#",
delimiter=' ',
create_using=None,
nodetype=None,
edgetype=None):
"""Read graph in multi-line adjacency list format from path.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_multiline_adjlist(G,"test.adjlist")
>>> G=nx.read_multiline_adjlist("test.adjlist")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.adjlist")
>>> G=nx.read_multiline_adjlist(fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_multiline_adjlist(G,"test.adjlist.gz")
>>> G=nx.read_multiline_adjlist("test.adjlist.gz")
nodetype is an optional function to convert node strings to nodetype
For example
>>> G=nx.read_multiline_adjlist("test.adjlist", nodetype=int)
will attempt to convert all nodes to integer type
Since nodes must be hashable, the function nodetype must return hashable
types (e.g. int, float, str, frozenset - or tuples of those, etc.)
edgetype is a function to convert edge data strings to edgetype
>>> G=nx.read_multiline_adjlist("test.adjlist", edgetype=int)
create_using is an optional networkx_v099 graph type, the default is
Graph(), a simple undirected graph
>>> G=nx.read_multiline_adjlist("test.adjlist", create_using=nx.DiGraph())
The comments character (default='#') at the beginning of a
line indicates a comment line.
The entries are separated by delimiter (default=' ').
If whitespace is significant in node or edge labels you should use
some other delimiter such as a tab or other symbol.
Example multiline adjlist file format
No edge data::
# source target for Graph or DiGraph
a 2
b
c
d 1
e
Wiht edge data::
# source target for XGraph or XDiGraph with edge data
a 2
b edge-ab-data
c edge-ac-data
d 1
e edge-de-data
Reading the file will use the default text encoding on your system.
It is possible to read files with other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
>>> fh=codecs.open("test.adjlist",'r',encoding='utf=8') # utf-8 encoding
>>> G=nx.read_multiline_adjlist(fh)
"""
if create_using is None:
G = networkx_v099.Graph()
else:
try:
G = create_using
G.clear()
except:
raise TypeError("Input graph is not a networkx_v099 graph type")
inp = _get_fh(path)
for line in inp:
# if line.startswith("#") or line.startswith("\n"):
# continue
# line=line.strip() #remove trailing \n
line = line[:line.find(comments)].strip()
if not line: continue
try:
(u, deg) = line.split(delimiter)
deg = int(deg)
except:
raise TypeError("Failed to read node and degree on line (%s)" %
line)
if nodetype is not None:
try:
u = nodetype(u)
except:
raise TypeError("Failed to convert node (%s) to type %s"\
%(u,nodetype))
G.add_node(u)
for i in range(deg):
line = inp.next().strip()
vlist = line.split(delimiter)
numb = len(vlist)
if numb > 0:
v = vlist[0]
if nodetype is not None:
try:
v = nodetype(v)
except:
raise TypeError("Failed to convert node (%s) to type %s"\
%(v,nodetype))
if numb == 1:
G.add_edge(u, v)
elif numb == 2:
d = vlist[1]
if edgetype is not None:
try:
d = edgetype(d)
except:
raise TypeError\
("Failed to convert edge data (%s) to type %s"\
%(d, edgetype))
G.add_edge(u, v, d)
else:
raise TypeError("Failed to read line: %s" % vlist)
return G
def read_leda(path):
"""Read graph in GraphML format from path.
Returns an XGraph or XDiGraph."""
fh = _get_fh(path, mode='r')
G = parse_leda(fh)
return G
def read_leda(path):
"""Read graph in GraphML format from path.
Returns an XGraph or XDiGraph."""
fh=_get_fh(path,mode='r')
G=parse_leda(fh)
return G
def write_gml(G, path):
"""
Write the graph G in GML format to the file or file handle path.
Examples
---------
>>> G=nx.path_graph(4)
>>> nx.write_gml(G,"test.gml")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.gml",'w')
>>> nx.write_gml(G,fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_gml(G,"test.gml.gz")
The output file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
>>> fh=codecs.open("test.gml",'w',encoding='iso8859-1')# use iso8859-1
>>> nx.write_gml(G,fh)
GML specifications indicate that the file should only use
7bit ASCII text encoding.iso8859-1 (latin-1).
Only a single level of attributes for graphs, nodes, and edges,
is supported.
"""
fh = _get_fh(path, mode='w')
# comments="#"
# pargs=comments+" "+' '.join(sys.argv)
# fh.write("%s\n" % (pargs))
# fh.write(comments+" GMT %s\n" % (time.asctime(time.gmtime())))
# fh.write(comments+" %s\n" % (G.name))
# check for attributes or assign empty dict
if hasattr(G, 'graph_attr'):
graph_attr = G.graph_attr
else:
graph_attr = {}
if hasattr(G, 'node_attr'):
node_attr = G.node_attr
else:
node_attr = {}
indent = 2 * ' '
count = iter(range(G.number_of_nodes()))
node_id = {}
fh.write("graph [\n")
# write graph attributes
for k, v in graph_attr.items():
if is_string_like(v):
v = '"' + v + '"'
fh.write(indent + "%s %s\n" % (k, v))
# write nodes
for n in G:
fh.write(indent + "node [\n")
# get id or assign number
if n in node_attr:
nid = node_attr[n].get('id', count.next())
else:
nid = count.next()
node_id[n] = nid
fh.write(2 * indent + "id %s\n" % nid)
fh.write(2 * indent + "label \"%s\"\n" % n)
if n in node_attr:
for k, v in node_attr[n].items():
if is_string_like(v): v = '"' + v + '"'
if k == 'id': continue
fh.write(2 * indent + "%s %s\n" % (k, v))
fh.write(indent + "]\n")
# write edges
for e in G.edges_iter():
if len(e) == 3:
u, v, d = e
# try to guess what is on the edge and do something reasonable
edgedata = {}
if d is None: # no data
pass
elif hasattr(d, 'iteritems'): # try dict-like
edgedata = dict(d.iteritems())
elif hasattr(d, '__iter__'): # some kind of container
edgedata['data'] = d.__repr__()
else: # something else - string, number
edgedata['data'] = d
else:
u, v = e
edgedata = {}
fh.write(indent + "edge [\n")
fh.write(2 * indent + "source %s\n" % node_id[u])
fh.write(2 * indent + "target %s\n" % node_id[v])
for k, v in edgedata.items():
if k == 'source': continue
if k == 'target': continue
if is_string_like(v): v = '"' + v + '"'
fh.write(2 * indent + "%s %s\n" % (k, v))
fh.write(indent + "]\n")
fh.write("]\n")
def write_multiline_adjlist(G, path, delimiter=' ', comments='#'):
"""
Write the graph G in multiline adjacency list format to the file
or file handle path.
See read_multiline_adjlist for file format details.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_multiline_adjlist(G,"test.adjlist")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.adjlist",'w')
>>> nx.write_multiline_adjlist(G,fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_multiline_adjlist(G,"test.adjlist.gz")
The file will use the default text encoding on your system.
It is possible to write files in other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
>>> fh=codecs.open("test.adjlist",'w',encoding='utf=8') # utf-8 encoding
>>> nx.write_multiline_adjlist(G,fh)
"""
fh = _get_fh(path, mode='w')
pargs = comments + " " + string.join(sys.argv, ' ')
fh.write("%s\n" % (pargs))
fh.write(comments + " GMT %s\n" % (time.asctime(time.gmtime())))
fh.write(comments + " %s\n" % (G.name))
def make_str(t):
if is_string_like(t): return t
return str(t)
if G.directed:
if G.multigraph:
for s, nbrs in G.adjacency_iter():
nbr_edges = [(u, d) for u, dl in nbrs.iteritems() for d in dl]
deg = len(nbr_edges)
fh.write(make_str(s) + delimiter + "%i\n" % (deg))
for u, d in nbr_edges:
if d is None:
fh.write(make_str(u) + '\n')
else:
fh.write(make_str(u) + delimiter + make_str(d) + "\n")
else: # directed single edges
for s, nbrs in G.adjacency_iter():
deg = len(nbrs)
fh.write(make_str(s) + delimiter + "%i\n" % (deg))
for u, d in nbrs.iteritems():
if d is None:
fh.write(make_str(u) + '\n')
else:
fh.write(make_str(u) + delimiter + make_str(d) + "\n")
else: #undirected
if G.multigraph:
seen = {} # helper dict used to avoid duplicate edges
for s, nbrs in G.adjacency_iter():
nbr_edges = [(u, d) for u, dl in nbrs.iteritems()
if u not in seen for d in dl]
deg = len(nbr_edges)
fh.write(make_str(s) + delimiter + "%i\n" % (deg))
for u, d in nbr_edges:
if d is None:
fh.write(make_str(u) + '\n')
else:
fh.write(make_str(u) + delimiter + make_str(d) + "\n")
seen[s] = 1
else: # undirected single edges
seen = {} # helper dict used to avoid duplicate edges
for s, nbrs in G.adjacency_iter():
nbr_edges = [(u, d) for u, d in nbrs.iteritems()
if u not in seen]
deg = len(nbr_edges)
fh.write(make_str(s) + delimiter + "%i\n" % (deg))
for u, d in nbr_edges:
if d is None:
fh.write(make_str(u) + '\n')
else:
fh.write(make_str(u) + delimiter + make_str(d) + "\n")
seen[s] = 1
def read_multiline_adjlist(path, comments="#", delimiter=' ',
create_using=None,
nodetype=None, edgetype=None):
"""Read graph in multi-line adjacency list format from path.
Examples
--------
>>> G=nx.path_graph(4)
>>> nx.write_multiline_adjlist(G,"test.adjlist")
>>> G=nx.read_multiline_adjlist("test.adjlist")
path can be a filehandle or a string with the name of the file.
>>> fh=open("test.adjlist")
>>> G=nx.read_multiline_adjlist(fh)
Filenames ending in .gz or .bz2 will be compressed.
>>> nx.write_multiline_adjlist(G,"test.adjlist.gz")
>>> G=nx.read_multiline_adjlist("test.adjlist.gz")
nodetype is an optional function to convert node strings to nodetype
For example
>>> G=nx.read_multiline_adjlist("test.adjlist", nodetype=int)
will attempt to convert all nodes to integer type
Since nodes must be hashable, the function nodetype must return hashable
types (e.g. int, float, str, frozenset - or tuples of those, etc.)
edgetype is a function to convert edge data strings to edgetype
>>> G=nx.read_multiline_adjlist("test.adjlist", edgetype=int)
create_using is an optional networkx_v099 graph type, the default is
Graph(), a simple undirected graph
>>> G=nx.read_multiline_adjlist("test.adjlist", create_using=nx.DiGraph())
The comments character (default='#') at the beginning of a
line indicates a comment line.
The entries are separated by delimiter (default=' ').
If whitespace is significant in node or edge labels you should use
some other delimiter such as a tab or other symbol.
Example multiline adjlist file format
No edge data::
# source target for Graph or DiGraph
a 2
b
c
d 1
e
Wiht edge data::
# source target for XGraph or XDiGraph with edge data
a 2
b edge-ab-data
c edge-ac-data
d 1
e edge-de-data
Reading the file will use the default text encoding on your system.
It is possible to read files with other encodings by opening
the file with the codecs module. See doc/examples/unicode.py
for hints.
>>> import codecs
>>> fh=codecs.open("test.adjlist",'r',encoding='utf=8') # utf-8 encoding
>>> G=nx.read_multiline_adjlist(fh)
"""
if create_using is None:
G=networkx_v099.Graph()
else:
try:
G=create_using
G.clear()
except:
raise TypeError("Input graph is not a networkx_v099 graph type")
inp=_get_fh(path)
for line in inp:
# if line.startswith("#") or line.startswith("\n"):
# continue
# line=line.strip() #remove trailing \n
line = line[:line.find(comments)].strip()
if not line: continue
try:
(u,deg)=line.split(delimiter)
deg=int(deg)
except:
raise TypeError("Failed to read node and degree on line (%s)"%line)
if nodetype is not None:
try:
u=nodetype(u)
except:
raise TypeError("Failed to convert node (%s) to type %s"\
%(u,nodetype))
G.add_node(u)
for i in range(deg):
line=inp.next().strip()
vlist=line.split(delimiter)
numb=len(vlist)
if numb>0:
v=vlist[0]
if nodetype is not None:
try:
v=nodetype(v)
except:
raise TypeError("Failed to convert node (%s) to type %s"\
%(v,nodetype))
if numb==1:
G.add_edge(u,v)
elif numb==2:
d=vlist[1]
if edgetype is not None:
try:
d=edgetype(d)
except:
raise TypeError\
("Failed to convert edge data (%s) to type %s"\
%(d, edgetype))
G.add_edge(u,v,d)
else:
raise TypeError("Failed to read line: %s"%vlist)
return G
def read_pajek(path):
"""Read graph in pajek format from path. Returns an XGraph or XDiGraph.
"""
fh = _get_fh(path, mode='r')
G = parse_pajek(fh)
return G
def read_edgelist(path, comments="#", delimiter=' ',
create_using=None, nodetype=None, edgetype=None):
"""Read a graph from a list of edges.
Parameters
----------
path : file or string
File or filename to write.
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 uses to separate values. The default is whitespace.
create_using : Graph container, optional
Use specified Graph container to build graph. The default is
nx.Graph().
nodetype : int, float, str, Python type, optional
Convert node data from strings to specified type
edgetype : int, float, str, Python type, optional
Convert edge data from strings to specified type
Returns
----------
out : graph
A networkx_v099 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")
>>> G=nx.read_edgelist(fh)
>>> G=nx.read_edgelist("test.edgelist", nodetype=int)
>>> G=nx.read_edgelist("test.edgelist",create_using=nx.DiGraph())
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 formats
Without edge data::
# source target
a b
a c
d e
With edge data:::
# source target data
a b 1
a c 3.14159
d e apple
"""
if create_using is None:
G=networkx_v099.Graph()
else:
try:
G=create_using
G.clear()
except:
raise TypeError("Input graph is not a networkx_v099 graph type")
fh=_get_fh(path)
for line in fh.readlines():
line = line[:line.find(comments)].strip()
if not len(line): continue
# if line.startswith("#") or line.startswith("\n"):
# continue
# line=line.strip() #remove trailing \n
# split line, should have 2 or three items
s=line.split(delimiter)
if len(s)==2:
if nodetype is not None:
try:
(u,v)=map(nodetype,s)
except:
raise TypeError("Failed to convert edge %s to type %s"\
%(s,nodetype))
else:
(u,v)=s
G.add_edge(u,v)
elif len(s)==3:
(u,v,d)=s
if nodetype is not None:
try:
(u,v)=map(nodetype,(u,v))
except:
raise TypeError("Failed to convert edge (%s, %s) to type %s"\
%(u,v,nodetype))
if d is not None and edgetype is not None:
try:
d=edgetype(d)
except:
raise TypeError("Failed to convert edge data (%s) to type %s"\
%(d, edgetype))
G.add_edge(u,v,d) # XGraph or XDiGraph
else:
raise TypeError("Failed to read line: %s"%line)
return G