From 600360961249509937446227a4967eaa721921ab Mon Sep 17 00:00:00 2001
From: Moria <moria@moria-research.(none)>
Date: Wed, 14 Oct 2015 11:34:59 -0400
Subject: [PATCH] Got edit distance working

---
 centerstar.py   | 91 +++++++++++++++++++++++++++++++++++++++++++++++++
 input.txt       |  6 ++++
 test_inputs.txt |  6 ++++
 3 files changed, 103 insertions(+)
 create mode 100644 input.txt
 create mode 100644 test_inputs.txt

diff --git a/centerstar.py b/centerstar.py
index e69de29..4134938 100644
--- a/centerstar.py
+++ b/centerstar.py
@@ -0,0 +1,91 @@
+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()
+
diff --git a/input.txt b/input.txt
new file mode 100644
index 0000000..44af585
--- /dev/null
+++ b/input.txt
@@ -0,0 +1,6 @@
+4
+AXZ
+AXXZ
+AYXYZ
+AYZ
+
diff --git a/test_inputs.txt b/test_inputs.txt
new file mode 100644
index 0000000..00e9261
--- /dev/null
+++ b/test_inputs.txt
@@ -0,0 +1,6 @@
+5
+CCTGCTGCAG
+GATGTGCCG
+GATGTGCAG
+CCGCTAGCAG
+CCTGTAGG