Convert tsv file so i can use it for nodes and edges in python

Question

I have this tsv file i would like to read and somehow count the numbers of nodes in a path

This is how the parts of tsv file looks like:

  6a3701d319fc3754  1297740409  166  14th_century;15th_century;16th_century;Pacific_Ocean;Atlantic_Ocean;Accra;Africa;Atlantic_slave_trade;African_slave_trade  NULL
  3824310e536af032  1344753412  88  14th_century;Europe;Africa;Atlantic_slave_trade;African_slave_trade 3

the paths is only the ones looking like this : 14th_century;15th_century; seperated by ';'

my code so fare :

import networkx as nx

fh = open("test.tsv", 'rb')
G = nx.read_edgelist("test.tsv", create_using=nx.DiGraph())
print G.nodes()
print G.edges()

So my question is how do i count the numbers of nodes touched by a path?

which parts are the nodes and edges here? Are you saying that this string 14th_century;15th_century;16th_century;Pacific_Ocean;Atlantic_Ocean;Accra;Africa;Atlantic_slave_trade;African_slave_trade needs to be parsed? Are these all edges or nodes? — EdChum
– EdChum, Commented Apr 5, 2014 at 21:06
the edge is the 14th.... and the nodes is the other ones if it gives any sense — Alexander Marcussen
– Alexander Marcussen, Commented Apr 6, 2014 at 11:06
So are you saying that in 14th_century;15th_century;16th_century;Pacific_Ocean;Atlantic_Ocean;Accra;Africa;Atlantic_slave_trade;African_slave_trade that 14th Century is connected to 15th, 16th century and also pacific ocean etc..? — EdChum
– EdChum, Commented Apr 6, 2014 at 14:49

EdChum · Accepted Answer · 2014-04-06 18:19:41Z

I'm using the pandas library here for speed, you can install using pip install pandas and also check here: http://pandas.pydata.org/

Firstly construct our dataframe from your sample code:

In [39]:

temp = """6a3701d319fc3754  1297740409  166  14th_century;15th_century;16th_century;Pacific_Ocean;Atlantic_Ocean;Accra;Africa;Atlantic_slave_trade;African_slave_trade  NULL

  3824310e536af032  1344753412  88  14th_century;Europe;Africa;Atlantic_slave_trade;African_slave_trade 3"""

# construct the dataframe
# in your case replace io.String() with the path to your tsv file
df = pd.read_csv(io.StringIO(temp), sep='\s+', header=None, names=['a','b','c','d','e'])

df
Out[39]:

                  a           b    c  \
0  6a3701d319fc3754  1297740409  166   
1  3824310e536af032  1344753412   88   

                                                   d   e  
0  14th_century;15th_century;16th_century;Pacific... NaN  
1  14th_century;Europe;Africa;Atlantic_slave_trad...   3  

[2 rows x 5 columns]

In [65]:

# use itertools to flatten our list of lists
import itertools

def to_edge_list(x):
    # split on semi-colon
    split_list = x.split(';')
    #print(split_list)
    # get our main node
    primary_node = split_list[0]
    # construct our edge list
    edge_list=[]
    # create a list comprehension from the split list
    edge_list = [(primary_node, x) for x in split_list[1:] ]
    #print(edge_list)
    return edge_list

# now use itertools to flatten the list of lists into a single list
combined_edge_list = list(itertools.chain.from_iterable(df['d'].apply(to_edge_list)))

print(combined_edge_list)

[('14th_century', '15th_century'), ('14th_century', '16th_century'), ('14th_century', 'Pacific_Ocean'), ('14th_century', 'Atlantic_Ocean'), ('14th_century', 'Accra'), ('14th_century', 'Africa'), ('14th_century', 'Atlantic_slave_trade'), ('14th_century', 'African_slave_trade'), ('14th_century', 'Europe'), ('14th_century', 'Africa'), ('14th_century', 'Atlantic_slave_trade'), ('14th_century', 'African_slave_trade')]

# Now construct our networkx graph from the edge list
In [66]:

import networkx as nx

G = nx.MultiDiGraph()
G.add_edges_from(combined_edge_list)
G.edges()


Out[66]:

[('14th_century', '15th_century'),
 ('14th_century', 'Africa'),
 ('14th_century', 'Africa'),
 ('14th_century', 'Atlantic_slave_trade'),
 ('14th_century', 'Atlantic_slave_trade'),
 ('14th_century', 'African_slave_trade'),
 ('14th_century', 'African_slave_trade'),
 ('14th_century', '16th_century'),
 ('14th_century', 'Accra'),
 ('14th_century', 'Europe'),
 ('14th_century', 'Atlantic_Ocean'),
 ('14th_century', 'Pacific_Ocean')]

draw the graph (doesn't look pretty but what the hell):

enter image description here

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