2

I have a directed, weighted network stored in a txt file as a list of 3 elements:

node1 node2 weight
node1 node3 weight
...

So for example the triplet:

1 10 50

means that I got an edge between node 1 and node 10 with weight 50.

Can someone please explain in detail how can I import this into graph tool to perform a community detection analysis using the SBM.

Thanks a lot.

Jose Ricardo Bustos M.
  • 8,016
  • 6
  • 40
  • 62
Ninja Warrior
  • 47
  • 8

2 Answers2

1

I assume that for a weighted graph you wish to use PropertyMaps (https://graph-tool.skewed.de/static/doc/quickstart.html#sec-property-maps)?

To import the file, you'll want to use file objects (https://docs.python.org/3/tutorial/inputoutput.html).

All together, the code you need is as follows:

#imports the graph-tools library
from graph_tool.all import *

#opens your file in mode "read"
f = open("your_file.txt","r")
#splits each line into a list of integers
lines = [[int(n) for n in x.split()] for x in f.readlines()]
#closes the file
f.close()

#makes the graph
g = Graph()
#adds enough vertices (the "1 + " is for position 0)
g.add_vertex(1 + max([l[0] for l in lines] + [l[1] for l in lines]))

#makes a "property map" to weight the edges
property_map = g.new_edge_property("int")
#for each line
for line in lines:
    #make a new edge
    g.add_edge(g.vertex(line[0]),g.vertex(line[1]))
    #weight it
    property_map[g.edge(g.vertex(line[0]),g.vertex(line[1]))] = line[2]
Benedict Randall Shaw
  • 728
  • 6
  • 15
1
graph_tool.load_graph_from_csv(file_name, csv_options={'delimiter': ' ', 'quotechar': '"'})

This will help you load a csv file with delimiter=space. I am still trying to read the documentation as to how to associate a weight to the edges: https://graph-tool.skewed.de/static/doc/graph_tool.html?highlight=load#graph_tool.Graph.load

Deeksha
  • 203
  • 5
  • 14