centerstar.py

import sys
import os
import itertools
import numpy as np


def find_edit_distance(v,w):
    '''
    Finds the edit distance between w and v
    Returns the distance between the two strings
    Edit graph is set up as w along y axis (left), v along x axis (top)
    Score 0 for match, 1 for mistmatch or indel
    '''
    # n, m are number of rows, cols
    # Note we need the +1 because we need to add the 0th row and column as our starting point
    # And python indexes at 0

    n = len(v)+1
    m = len(w)+1

    # Init graph
    edit_graph = np.zeros((n, m)) 
    
    # Add distances along x, y axis
    # +1 at every step because indels -> +1
    for i in range(n):
        edit_graph[i,0] = i
    for j in range(m):
        edit_graph[0,j] = j

    # Go through the graph
    for i in range(1, n):
        for j in range(1,m):
            
            # Get the diag distance
            if v[i-1] == w[j-1]:
                diag = edit_graph[i-1,j-1]
            else:
                diag = edit_graph[i-1,j-1] + 1
            
            # Update
            edit_graph[i,j] = min(edit_graph[i-1, j]+1, edit_graph[i,j-1]+1, diag)
    
    # Return n,m 
    distance = edit_graph[n-1,m-1]
    return distance



def main():
    '''
    Main Function
    '''

    # Try to get file as input
    try:
        input_file = sys.argv[1]
    except:
        print "Please supply an input file"
        sys.exit()


    # Read in n, strings to S
    with open(input_file, 'r') as f:
        content = f.readlines()
    
    n = int(content[0].strip())
    S = [s.strip() for s in content[1:]]

    # Init scoring table to find center string candidate
    scores = [0 for i in range(n)]

    # Create all index pairs of strings to score
    string_pairs = itertools.combinations(range(n), 2)
    
    # Iterate and score
    for pair in string_pairs:
        w = S[pair[0]]
        v = S[pair[1]]
        distance = find_edit_distance(w,v)
        
        # Update scores
        for i in range(n):
            if i in pair:
                scores[i] += distance

    

if __name__ == '__main__':
    main()