Deso je sais pas si ca compile

alignementseq.py

@@ -41,15 +41,15 @@ def align(seq1, seq2):
     y = seq2.seq
     n=len(x)
     m=len(y)
-    mat = [[0 for _ in range(m+1)] for _ in range(n+1)]   # scores matrix
+    mm = [[0 for _ in range(m+1)] for _ in range(n+1)]   # scores matrix
     path = [[0 for _ in range(m+1)] for _ in range(n+1)]   # last step for optimal score
     
     # first line and col
     for i in range(1, n+1):
-        mat[i][0] = mat[i-1][0] + score('', x[i-1])
+        mm[i][0] = mm[i-1][0] + score('', x[i-1])
         path[i][0] = (i-1, 0)
     for j in range(1, m+1):
-        mat[0][j] = mat[j-1][0] + score('', y[j-1])
+        mm[0][j] = mm[j-1][0] + score('', y[j-1])
         path[0][j] = (0, j-1)
     
     # fill table
@@ -57,25 +57,115 @@ def align(seq1, seq2):
         for j in range(1, m+1):
             a = x[i-1]
             b = y[j-1]
-            s1 = mat[i-1][j-1] + score(a,b)
-            s2 = mat[i-1][j] + score('', a)
-            s3 = mat[i][j-1] + score('', b)
+            s1 = mm[i-1][j-1] + score(a,b)
+            s2 = mm[i-1][j] + score('', a)
+            s3 = mm[i][j-1] + score('', b)
             if s1 >= s2:
                 if s1 >= s3:
-                    mat[i][j] = s1
+                    mm[i][j] = s1
                     path[i][j] = (i-1, j-1)
                 else:
-                    mat[i][j] = s3
+                    mm[i][j] = s3
                     path[i][j] = (i, j-1)
             else:   # s2 > s1
                 if s2 >= s3:
-                    mat[i][j] = s2
+                    mm[i][j] = s2
                     path[i][j] = (i-1, j)
                 else:
-                    mat[i][j] = s3
+                    mm[i][j] = s3
                     path[i][j] = (i, j-1)
     
-    bestScore = mat[n][m]
+    bestScore = mm[n][m]
+    alx = ""
+    aly = ""
+    i, j = n, m
+    while i > 0 and j > 0:
+        i2, j2 = path[i][j]
+        if i==i2:
+            alx+='-'
+        else:
+            alx+=x[i-1]
+        if j==j2:
+            aly+='-'
+        else:
+            aly+=y[j-1]
+        i,j = i2, j2
+    while i>0:
+        aly+='-'
+        alx+=x[i-1]
+        i -=1
+    while j>0:
+        alx+='-'
+        aly+=y[j-1]
+        j -=1
+    alx = alx[::-1]
+    aly = aly[::-1]
+    seq1.seq = Seq(alx)
+    seq2.seq = Seq(aly)
+    return bestScore, seq1, seq2
+
+
+def align2steps(seq1, seq2, d=8, e=4):
+    x = seq1.seq
+    y = seq2.seq
+    n=len(x)
+    m=len(y)
+    mm = [[0 for _ in range(m+1)] for _ in range(n+1)]   # scores matrix
+    mx = [[0 for _ in range(m+1)] for _ in range(n+1)]
+    my = [[0 for _ in range(m+1)] for _ in range(n+1)]
+    path = [[0 for _ in range(m+1)] for _ in range(n+1)]   # last step for optimal score
+    
+    # first line and col
+    for i in range(1, n+1):
+        mx[i][1] = my[i][1] = -d -(i-1)*e
+        path[i][0] = (i-1, 0)
+    for j in range(1, m+1):
+        mx[1][j] = my[1][i] = -d - (j-1)*e
+        path[0][j] = (0, j-1)
+    
+    # fill table
+    for i in range(2, n+1):
+        for j in range(2, m+1):
+            a = x[i-1]
+            b = y[j-1]
+            
+            # find max for M
+            s1 = mm[i-1][j-1] + score(a,b)
+            s2 = mx[i-1][j-1] + score(a,b)
+            s3 = my[i][j-1] + score(a,b)
+            
+            if s1 >= s2:
+                if s1 >= s3:
+                    mm[i][j] = s1
+                    path[i][j] = (i-1, j-1)
+                else:
+                    mm[i][j] = s3
+                    path[i][j] = (i, j-1)
+            else:   # s2 > s1
+                if s2 >= s3:
+                    mm[i][j] = s2
+                    path[i][j] = (i-1, j)
+                else:
+                    mm[i][j] = s3
+                    path[i][j] = (i, j-1)
+            
+            # find max for I_x
+            s4 = mm[i-1][j] - d
+            s5 = mx[i-1][j] - e
+            if s4 >= s5:
+                mx[i][j] = s4
+            else:
+                mx[i][j] = s5
+            
+            # find max for I_y
+            s6 = mm[i][j-1] - d
+            s7 = my[i][j-1] - e
+            if s6 >= s7:
+                my[i][j] = s6
+            else:
+                my[i][j] = s7
+    
+    bestScore = mm[n][m]
     alx = ""
     aly = ""
     i, j = n, m