Sourcery Starbot ⭐ refactored A-F-V/Bioinformatics by SourceryAI · Pull Request #7 · A-F-V/Bioinformatics

SourceryAI · 2024-02-17T17:51:03Z

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SourceryAI · 2024-02-17T17:51:04Z

bioinformatics/algorithms/alignment_graph.py

-            o = []
-            for c in range(len(self.s2)+1):
-                o.append(self.pos(r,c))
+            o = [self.pos(r,c) for c in range(len(self.s2)+1)]


Function Alignment_Graph.prnt refactored with the following changes:

Convert for loop into list comprehension (list-comprehension)

SourceryAI · 2024-02-17T17:51:05Z

bioinformatics/algorithms/binary_search.py

+            elif first:
+                if mid == self.start or self.comparer(self.emitter(mid-1)) != 0:
+                    return mid
                else:
-                    if mid == self.end or self.comparer(self.emitter(mid+1)) != 0:
-                        return mid
-                    left = mid
+                    right = mid
+            elif mid == self.end or self.comparer(self.emitter(mid+1)) != 0:
+                return mid
+            else:
+                left = mid


Function BinarySearch.search refactored with the following changes:

Merge else clause's nested if statement into elif [×2] (merge-else-if-into-elif)

Lift code into else after jump in control flow [×2] (reintroduce-else)

SourceryAI · 2024-02-17T17:51:05Z

bioinformatics/algorithms/binary_tree.py

        self.edges = edges # a dict of node name to a list of neighbours (child name, edgeval)
        self.root = root #the name of the root
-        if self.root ==None:
+        if self.root is None:


Function BinaryTree.__init__ refactored with the following changes:

Use x is None rather than x == None (none-compare)

SourceryAI · 2024-02-17T17:51:05Z

bioinformatics/algorithms/binary_tree.py

        if node == "ROOT":
            return self.leaves(self.root)
-        if node==None:
+        if node is None:


Function BinaryTree.leaves refactored with the following changes:

Use x is None rather than x == None (none-compare)

SourceryAI · 2024-02-17T17:51:05Z

bioinformatics/algorithms/binary_tree.py

-        else:
-            ln,lw = self.left(node)
-            rn,rw = self.right(node)
-            return lw+rw+self.edgecost(ln)+self.edgecost(rn)
+        ln,lw = self.left(node)
+        rn,rw = self.right(node)
+        return lw+rw+self.edgecost(ln)+self.edgecost(rn)


Function BinaryTree.edgecost refactored with the following changes:

Remove unnecessary else after guard condition (remove-unnecessary-else)

SourceryAI · 2024-02-17T17:51:05Z

bioinformatics/algorithms/four_russians_binary_encoding.py

-                if top==None:
+                if top is None:
                    graph.set(r,c,graph.pos(r,c-1)+indel,2)
                else:
                    graph.set(r,c,top[c-1])
            elif c==0:
-                if left==None:
+                if left is None:


Function fill_graph_needleman refactored with the following changes:

Use x is None rather than x == None [×2] (none-compare)

SourceryAI · 2024-02-17T17:51:06Z

bioinformatics/algorithms/four_russians_binary_encoding.py

-        for i in range(self.t):
-            output += random.choice(self.chars)
-        return output
+        return "".join(random.choice(self.chars) for _ in range(self.t))


Function Sequence.random refactored with the following changes:

Use str.join() instead of for loop (use-join)

Replace unused for index with underscore (for-index-underscore)

Inline variable that is immediately returned (inline-immediately-returned-variable)

SourceryAI · 2024-02-17T17:51:06Z

bioinformatics/algorithms/four_russians_binary_encoding.py

-        for ind in range(self.t):
+        for _ in range(self.t):


Function Sequence.objWithNum refactored with the following changes:

Replace unused for index with underscore (for-index-underscore)

SourceryAI · 2024-02-17T17:51:06Z

bioinformatics/algorithms/four_russians_binary_encoding.py

-        if len(o) > 0:
+        if o:


Function accumulate_diff refactored with the following changes:

Simplify sequence length comparison (simplify-len-comparison)

SourceryAI · 2024-02-17T17:51:06Z

bioinformatics/algorithms/hmm.py

-        if key == "END":
-            return self.graph[len(self.x)+1, "END"]
-        return self.graph[key]
+        return self.graph[len(self.x)+1, "END"] if key == "END" else self.graph[key]


Function ViterbiGraph.__getitem__ refactored with the following changes:

Lift code into else after jump in control flow (reintroduce-else)

Replace if statement with if expression (assign-if-exp)

SourceryAI · 2024-02-17T17:51:07Z

bioinformatics/algorithms/middle_node.py

-    if (a,b) in blosum62:
-        return blosum62[(a,b)]
-    return blosum62[(b,a)]
+    return blosum62[(a,b)] if (a,b) in blosum62 else blosum62[(b,a)]


Function blosum62score refactored with the following changes:

Lift code into else after jump in control flow (reintroduce-else)

Replace if statement with if expression (assign-if-exp)

SourceryAI · 2024-02-17T17:51:08Z

bioinformatics/algorithms/middle_node.py

-    for i in range(1,col+1):
+    for _ in range(1,col+1):
        c2 = [c1[0]+indel]
-        for row in range(1,height+1):
-            c2.append(max(c2[row-1]+indel,c1[row]+indel,c1[row-1]+blosum62score(s1[row-1],s2[col-1])))
+        c2.extend(
+            max(
+                c2[row - 1] + indel,
+                c1[row] + indel,
+                c1[row - 1] + blosum62score(s1[row - 1], s2[col - 1]),
+            )
+            for row in range(1, height + 1)
+        )


Function prefix refactored with the following changes:

Replace unused for index with underscore (for-index-underscore)

Replace a for append loop with list extend (for-append-to-extend)

SourceryAI · 2024-02-17T17:51:08Z

bioinformatics/algorithms/middle_node.py

-    f = open(filei,"r")
-    w1 = f.readline().rstrip('\n')
-    w2 = f.readline().rstrip('\n')
-    f.close()
+    with open(filei,"r") as f:
+        w1 = f.readline().rstrip('\n')
+        w2 = f.readline().rstrip('\n')
    o  = func(w1,w2)
-    f = open(filej,"w")
-    f.writelines(str(o))
-    f.close()
+    with open(filej,"w") as f:
+        f.writelines(str(o))


Function rosalind refactored with the following changes:

Use with when opening file to ensure closure [×2] (ensure-file-closed)

SourceryAI · 2024-02-17T17:51:08Z

bioinformatics/algorithms/needleman_wunsch.py

-            o1 = "-"+o1
+            o1 = f"-{o1}"
            o2 = graph.s2[c-1]+o2
            pointer = (r,c-1)
        elif p==1:
            o1 = graph.s1[r-1]+o1
-            o2 = "-"+o2
+            o2 = f"-{o2}"


Function trace_pointers_needleman refactored with the following changes:

Use f-string instead of string concatenation [×2] (use-fstring-for-concatenation)

SourceryAI · 2024-02-17T17:51:08Z

bioinformatics/algorithms/neighbour_joining.py



-def neighbour_joining(d_mat: DistanceMatrix, inner_node_next_label=None):  # DO NOT USE heaping distance matrix
+def neighbour_joining(d_mat: DistanceMatrix, inner_node_next_label=None):    # DO NOT USE heaping distance matrix


Function neighbour_joining refactored with the following changes:

Replace unneeded comprehension with generator (comprehension-to-generator)

SourceryAI · 2024-02-17T17:51:09Z

bioinformatics/algorithms/suffix_array.py

+
        searcher = BinarySearch(0, len(self.indices)-1, comparer, emitter=self.suffix)
        frm, to = searcher.search(first=True), searcher.search(first=False)
-        if frm == None or to == None:
+        if frm is None or to is None:


Function SuffixArray.find_matching_pattern refactored with the following changes:

Use x is None rather than x == None [×2] (none-compare)

SourceryAI · 2024-02-17T17:51:09Z