Finish Week 2 Tasks

Code/ApproximatePatternCount.py

@@ -0,0 +1,16 @@
+def ApproximatePatternCount(Pattern, Text, d):
+    count = 0
+    for i in range(len(Text)-len(Pattern)+1):
+        if Text[i:i+len(Pattern)] == Pattern:
+            count += 1
+        elif HammingDistance(Text[i:i+len(Pattern)], Pattern) <= d:
+            count += 1
+    return count
+
+
+def HammingDistance(p, q):
+    count = 0
+    for i in range(0, len(p)):
+        if p[i] != q[i]:
+            count += 1
+    return count

Code/ApproximatePatternMatching.py

@@ -0,0 +1,16 @@
+def ApproximatePatternMatching(Text, Pattern, d):
+    positions = []
+    for i in range(len(Text)-len(Pattern)+1):
+        if Text[i:i+len(Pattern)] == Pattern:
+            positions.append(i)
+        elif HammingDistance(Text[i:i+len(Pattern)], Pattern) <= d:
+            positions.append(i)
+    return positions
+
+
+def HammingDistance(p, q):
+    count = 0
+    for i in range(0, len(p)):
+        if p[i] != q[i]:
+            count += 1
+    return count

Code/FasterSymbolArray.py

@@ -0,0 +1,20 @@
+def FasterSymbolArray(Genome, symbol):
+    array = {}
+    n = len(Genome)
+    ExtendedGenome = Genome + Genome[0:n//2]
+    array[0] = PatternCount(symbol, Genome[0:n//2])
+    for i in range(1, n):
+        array[i] = array[i-1]
+        if ExtendedGenome[i-1] == symbol:
+            array[i] = array[i]-1
+        if ExtendedGenome[i+(n//2)-1] == symbol:
+            array[i] = array[i]+1
+    return array
+
+
+def PatternCount(Text, Pattern):
+    count = 0
+    for i in range(len(Text)-len(Pattern)+1):
+        if Text[i:i+len(Pattern)] == Pattern:
+            count = count+1
+    return count

Code/HammingDistance.py

@@ -0,0 +1,6 @@
+def HammingDistance(p, q):
+    count = 0
+    for i in range(0, len(p)):
+        if p[i] != q[i]:
+            count += 1
+    return count

Code/MinimumSkew.py

@@ -0,0 +1,21 @@
+def MinimumSkew(Genome):
+    positions = []
+    skew = SkewArray(Genome)
+    minimum = min(skew)
+    for i in range(0, len(Genome)):
+        if skew[i] == minimum:
+            positions.append(i)
+    return positions
+
+
+def SkewArray(Genome):
+    Skew = []
+    Skew.append(0)
+    for i in range(0, len(Genome)):
+        if Genome[i] == "G":
+            Skew.append(Skew[i] + 1)
+        elif Genome[i] == "C":
+            Skew.append(Skew[i] - 1)
+        else:
+            Skew.append(Skew[i])
+    return Skew

Code/SkewArray.py

@@ -0,0 +1,11 @@
+def SkewArray(Genome):
+    Skew = []
+    Skew.append(0)
+    for i in range(0, len(Genome)):
+        if Genome[i] == "G":
+            Skew.append(Skew[i] + 1)
+        elif Genome[i] == "C":
+            Skew.append(Skew[i] - 1)
+        else:
+            Skew.append(Skew[i])
+    return Skew

Code/SymbolArray.py

@@ -0,0 +1,15 @@
+def SymbolArray(Genome, symbol):
+    array = {}
+    n = len(Genome)
+    ExtendedGenome = Genome + Genome[0:n//2]
+    for i in range(n):
+        array[i] = PatternCount(ExtendedGenome[i:i+(n//2)], symbol)
+    return array
+
+
+def PatternCount(Text, Pattern):
+    count = 0
+    for i in range(len(Text)-len(Pattern)+1):
+        if Text[i:i+len(Pattern)] == Pattern:
+            count = count+1
+    return count