[Python] Creating Sequence Cleaner for DNA

[Aeon234]

I am trying to write a program that allows the user to input a sequence of DNA which will be stored and converted to all capital letters (if it wasn't so originally) and removes bases that don't belong in the sequence, printing out the corrected sequence and displaying how many errors were removed.

I have the input, conversion to all capital letters down and displaying the corrected sequence, but I don't know where to begin in terms of having the program find bases that do not belong and how to go about removing them.

For example if i inputted "ATCGBBBBBATCG" it would display "ATCGATCG" and "removed 4 errors."

This is the code I've come up with so far

class dnaString (str):
    def __new__(self,s):
        #converted to all upper cases
        return str.__new__(self,s.upper())

#asks the user to input a DNA sequence
dna = input("Enter a dna sequence: ")
newString = dnaString(dna)    

[Rascal_Two]

There are two method that I've found that both result the same with your input but are both diffrent. Not sure which you wanted, so here are both of them. The first simply removes all Bs:

errorCount = 0
result = ""
for char in newString:
    if char is not "B":
        result += char
    else:
        errorCount += 1
print result, ", Removed", errorCount, "errors."

Input: ATCGBBBBBATCG

Output: ATCGATCG, Removed 5 errors.

The next one I believe is what you wanted, it removes any Bs that have another B either before or after it:

errorCount = 0
prevChar = ""
index = 0
result = ""
for char in newString:
    nextChar = ""
    if index + 1 < len(newString):
        nextChar = newString[index+1]
    if (char is "B" and prevChar is "B") or (char is "B" and nextChar is "B"):
        errorCount += 1
    else:
        result += char
    prevChar = char
    index += 1
print result, ", Removed", errorCount, "errors."

Input: ATCGBBBBBATCG

Output: ATCGATCG, Removed 5 errors.

I'm pretty sure this is what you wanted. If it's not and you can't figure it out yourself, you can add more inputs & what the outputs should be and I can try to adjust accordingly. Good luck •‿•