medianSearch

medianSearch.py

@@ -0,0 +1,70 @@
+from itertools import product
+
+
+def hamming(string1, string2):
+    result = 0
+    for c1, c2 in zip(string1, string2):
+        if c1 != c2:
+            result += 1
+    return result
+
+
+def distance(Xi, word):
+    j = len(word)
+    result = len(word)
+    for i in range(len(Xi) - j):
+        #print("Comparing " + str(Xi[i:j+i]) + " to " + str(word)  + " result " + str(hamming(Xi[i:j+i], word)))
+        hamm = hamming(Xi[i:j+i], word)
+        if result > hamm:
+            result = hamm
+    return result
+
+
+def distance2(Xi, word):
+    j = len(word)
+    result = len(word)
+    for i in range(len(Xi) - j):
+        hamm = hamming(Xi[i:j+i], word)
+        if result > hamm:
+            result = hamm
+            motif = Xi[i:j+i]
+    return motif
+
+X = ["CCTGATAGACGCTATCTGGCTATCCAGGTACTTAGGTCCTCTGTGCGAATCTATGCGTTTCCAACCAT",
+     "AGTACTGGTGTACATTTGATCCATACGTACACCGGCAACCTGAAACAAACGCTCAGAACCAGAAGTGC",
+     "AAACGTTAGTGCACCCTCTTTCTTCGTGGCTCTGGCCAACGAGGGCTGATGTATAAGACGAAAATTTT",
+     "AGCCTCCGATGTAAGTCATAGCTGTAACTATTACCTGCCACCCCTATTACATCTTACGTCCATATACA",
+     "CTGTTATACAACGCGTCATGGCGGGGTATGCGTTTTGGTCGTCGTACGCTCGATCGTTACCGTACGGC"]
+
+
+l = 8
+t = len(X)
+best = l+1
+
+
+for permutation in product("ACGT", repeat=l):
+    word = ''.join(permutation)
+    for i in range(1, l+1):
+        if i < l:
+            prefix = word[:i]
+            optimistic = 0
+            for t in X:
+                optimistic += distance(t, prefix)
+            if optimistic > best:
+                break
+            else:
+                i += 1
+        else:
+            score = 0
+            for t in X:
+                score += distance(t, word)
+            if score < best:
+                best = score
+                median = word
+
+print("Motif: ", median, "with score: ", best)
+
+
+for t in X:
+        print(distance2(t, median))
+