weka511#29 Cosmetic changes

Author: weka511

BA5L.py

@@ -28,17 +28,12 @@
 #
 # Inputs: v
 #         w
+#         replace_score
+#         indel_cost
 
-def alignUsingLinearSpace(v,w,replace_score=substitution_matrices.load("BLOSUM62"),indel_cost=5):
-    # LinearSpaceAlignment
-    #
-    # Find longest path between a substring of v[top] v[bottom-1]
-    # and w[left] and w[right-1]
-    #
-    # Inputs: top
-    #         bottom
-    #         left
-    #         right
+def alignUsingLinearSpace(v,w,
+                          replace_score = substitution_matrices.load("BLOSUM62"),
+                          indel_cost    = 5):
 
     def isRightOrDownRight(midEdge):
         return midEdge==RIGHT or midEdge==DOWNRIGHT
@@ -54,6 +49,15 @@ def MiddleNodeAndEdge(top, bottom, left, right):
         direction         = RIGHT if i1==i2 else DOWN if j1==j2 else DOWNRIGHT
         return j1,direction
 
+    # LinearSpaceAlignment
+    #
+    # Find longest path between a substring of v[top] v[bottom-1]
+    # and w[left] and w[right-1]
+    #
+    # Inputs: top
+    #         bottom
+    #         left
+    #         right
 
     def  LinearSpaceAlignment(top, bottom, left, right):
         if left==right:
@@ -74,7 +78,7 @@ def  LinearSpaceAlignment(top, bottom, left, right):
     RIGHT     = 0
     DOWN      = 1
     DOWNRIGHT = 2
-    LinearSpaceAlignment(0,len(v),0,len(w))
+    LinearSpaceAlignment(0,len(v)+1,0,len(w)+1)
 
 
 if __name__=='__main__':

align.py

@@ -657,10 +657,10 @@ def explore(s,t,limit):
 
     middle_column = len(t)//2  
     from_source,_ = explore(s,t,middle_column)
-    to_sink,_   = explore(s[::-1],t[::-1],len(t) - middle_column)
+    to_sink,_     = explore(s[::-1],t[::-1],len(t) - middle_column)
     length        = [a+b for (a,b) in zip(from_source,to_sink[::-1])]
 
-    return ((argmax(length), middle_column),
+    return ((argmax(length),   middle_column),
             (argmax(length)+1, middle_column+1))
 
 # FindHighestScoringMultipleSequenceAlignment