Optimizing a code

[perfringo]

Following is based on opening statement: "I create an algorithm that will give me the path of the shortest interactions between 2 proteins".

I would read data from file into dictionary or defaultdict so that key is node and values are edges.

With dictionary:

data = dict()                                                              
with open('proteins.txt', 'r') as f: 
    for row in f: 
        k, v = row.strip().split() 
        data.setdefault(k, set()).add(v)

Or with defauldict:

data = defaultdict(set)
with open('proteins.txt', 'r') as f: 
    for row in f: 
        k, v = row.strip().split() 
        data[k].add(v)

Now when I have data nicely structured I implement shortest path algorithm. You can find one from python. org: Python Patterns - Implementing Graphs.