Create SeqModification.py

Author: mchunn-1

SeqModification.py

@@ -0,0 +1,52 @@
+
+#def indicates that it is a function definition
+def partA(gcCount): 
+    #sets teh variable count = to 0 so it can be added to 
+    count = 0
+    for i in gcCount:
+        #looks for all indications of G and C
+        if i == "G" or i =="C":
+                #adds 1 to the count variable when a G/C is found 
+                count = count + 1 
+    #returns the number of G/C bases
+    return count 
+
+#built-in random variable generator 
+import random 
+
+def partB(seq):
+    #reads the file 
+    seq1 = seq.read()
+    #puts it into lowercase
+    seq1 = seq1.lower()
+    bases = ['A','T','C','G']
+    num = input("Please input an integer ")
+    num = int(num)
+    for i in range(num):
+        #determines a random postion in the file of bases and then replaces the base with a random base
+        ranPosition = random.randint(0, len(seq1)-1)
+        print("The nucleotide at the random postion " + str(ranPosition) + " was replaced")
+        baseFin = random.choice(bases)
+        seq2 = seq1[:ranPosition] + baseFin + seq1[ranPosition +1:]
+    #returns thhe modified file 
+    return(seq2) 
+
+def main():
+    seqGC = input('Please enter a sequence of bases. The G and C bases will be counted.')
+    finCount = partA(seqGC)
+    #str() converts the integer from the input to a string 
+    print("The GC count is " + str(finCount))
+    fileName = input("Please enter a file name ")
+    #will try to open the file name thhat was input
+    try:
+        seq = open(fileName)
+    #if the file cannot be opened the the print statement will run
+    except:
+        print("File cannot be read. Please try again.")
+        exit()
+    seq2 = partB(seq)
+    print(seq2)
+
+
+if __name__ == "__main__":
+	main()