In [1]:

    

!python --version


    

    




Python 3.5.2 :: Anaconda 4.2.0 (x86_64)

In [2]:

    

import pandas as pd
import json


    

In [23]:

    

net = pd.read_csv('./sample-simulation/testNetwork.txt', delimiter='\t')
net.head(20)


    

    
Out[23]:






  

    

      

      
Source
      
Target
    
  
  

    

      
0
      
YJL166W
      
GO:0006122
    
    

      
1
      
YEL024W
      
GO:0006122
    
    

      
2
      
GO:0005739
      
GO:0005750
    
    

      
3
      
GO:0009167
      
GO:0009123
    
    

      
4
      
GO:0044281
      
GO:0044710
    
    

      
5
      
GO:0009161
      
GO:0009167
    
    

      
6
      
GO:1901360
      
GO:0071704
    
    

      
7
      
GO:0044710
      
GO:0044699
    
    

      
8
      
GO:0005750
      
GO:1902495
    
    

      
9
      
GO:0022900
      
GO:0044763
    
    

      
10
      
GO:0022904
      
GO:0022900
    
    

      
11
      
GO:1902495
      
GO:0044425
    
    

      
12
      
GO:0044425
      
GO:0005575
    
    

      
13
      
GO:0008150
      
GO:00SUPER
    
    

      
14
      
GO:0008152
      
GO:0044710
    
    

      
15
      
GO:0006753
      
GO:0055086
    
    

      
16
      
GO:0009123
      
GO:0006753
    
    

      
17
      
GO:0044699
      
GO:0008150
    
    

      
18
      
GO:0044763
      
GO:0044699
    
    

      
19
      
GO:0055086
      
GO:0044763
    
  

In [24]:

    

prop = pd.read_csv('./sample-simulation/testNetwork_style.txt', delimiter='\t')
prop.head()


    

    
Out[24]:






  

    

      

      
Source
      
Property
    
  
  

    

      
0
      
YJL166W
      
1.000000
    
    

      
1
      
GO:0006122
      
0.444456
    
    

      
2
      
YEL024W
      
1.000000
    
    

      
3
      
GO:0005739
      
0.191416
    
    

      
4
      
GO:0005750
      
0.360780
    
  

In [13]:

    

prop[prop['Source'] =='YEL024W']


    

    
Out[13]:






  

    

      

      
Source
      
Property
    
  
  

    

      
2
      
YEL024W
      
1.0
    
  

In [3]:

    

subnet = {
    'data': {
        'name': 'simulation1'
    },
    'elements': {
        'nodes': [],
        'edges': []
    }
}

def get_node(id, score):
    node = {
        'data': {
            'id': id,
            'score': score
        }
    }  
    return node

def get_edge(source, target):
    edge = {
        'data': {
            'source': source,
            'target': target
        }
    }
    
    return edge


    

In [26]:

    

for data in net.iterrows():
    row=data[1]
    edge = get_edge(row['Source'], row['Target'])
    subnet['elements']['edges'].append(edge)

for data in prop.iterrows():
    row=data[1]
    node = get_node(row['Source'], row['Property'])
    subnet['elements']['nodes'].append(node)

with open('./data/subnet.cyjs', 'w') as outfile:
    json.dump(subnet, outfile)


    

In [1]:

    

# Load from NetworkX JSON

import json
from pprint import pprint

with open('./data/YAL056W_YCL038C.json') as data_file:    
    result1 = json.load(data_file)
    
with open('./data/YBL098W_YPL113C.json') as data_file:    
    result2 = json.load(data_file)

pprint(result1)


    

    




{'directed': False,
 'edges': [{'source': 'GO:0016020', 'target': 'GO:0005575'},
           {'source': 'GO:0044464', 'target': 'GO:0005575'},
           {'source': 'GO:0044464', 'target': 'GO:0044424'},
           {'source': 'GO:0005575', 'target': 'GO:00SUPER'},
           {'source': 'GO:0044444', 'target': 'GO:0044424'},
           {'source': 'GO:0044444', 'target': 'YAL056W'},
           {'source': 'GO:0044444', 'target': 'YCL038C'},
           {'source': 'GO:0008150', 'target': 'GO:0044699'},
           {'source': 'GO:0008150', 'target': 'GO:00SUPER'}],
 'graph': {},
 'multigraph': False,
 'nodes': [{'id': 'GO:0016020',
            'importance': 0.0,
            'phenotype': 0.024179171770811},
           {'id': 'GO:0044464', 'importance': 0.0, 'phenotype': 'NA'},
           {'id': 'GO:0005575', 'importance': 0.0, 'phenotype': 'NA'},
           {'id': 'GO:0044444',
            'importance': 0.0,
            'phenotype': 0.01525542512536},
           {'id': 'YCL038C', 'importance': 0.0, 'phenotype': 0.0},
           {'id': 'GO:0008150', 'importance': 0.0, 'phenotype': 'NA'},
           {'id': 'GO:0044424', 'importance': 0.0, 'phenotype': 'NA'},
           {'id': 'YAL056W', 'importance': 0.0, 'phenotype': 0.0},
           {'id': 'GO:0044699',
            'importance': 0.0,
            'phenotype': 0.01524106413126},
           {'id': 'GO:00SUPER',
            'importance': 0.0,
            'phenotype': 0.024996409192681}]}

In [10]:

    

nodes1 = result1['nodes']
edges1 = result1['edges']
new_nodes1 = []
new_edges1 = []

for node in nodes1:
    new_nodes1.append(get_node(node['id'], node['phenotype']))
    
for edge in edges1:
    new_edges1.append(get_edge(edge['source'], edge['target']))
    
net1 = {
    'data': {'name': 'result1'},
    'elements': {
        'nodes': new_nodes1,
        'edges': new_edges1
    }
}

with open('./data/result1.cyjs', 'w') as outfile:
    json.dump(net1, outfile)