CODEWITHSUNDEEP
python
bk88
bk88

Reputation: 5

how to use loops to compare sequences?

I am trying to compare the two sequences, a and b, and write code that prints out where these mismatches are. I know the code below is not correct, but it is the closest I can come for the sake of this. I feel I am misunderstanding something about the concept of flow. Any help would be greatly appreciated. Thanks.

a="CATCGTCCT"
b="CACCGACCG"
mismatch_seq=[]
for x in list(a):
    mismatch=[]
    if x!=x in list(b):
        mismatch+=x in list(b)
        mismatch_seq.append(mismatch)
    else:
       pass
print mismatch_seq

EDIT: In addition, how would you write code to tell you where, in terms of index, this mismatch occurred?

Upvotes: 0

Views: 175

Answers (4)

ssm
ssm

Reputation: 5373

You can just use the following: 

>>> filter(lambda m: m[1][0] != m[1][1] , enumerate(zip(a, b)))
[(2, ('T', 'C')), (5, ('T', 'A')), (8, ('T', 'G'))]

I would recommend using izip. This way you can put in entire files which are arbitrarily long, and then can safely send the output to a file ...

Upvotes: 1

icedwater
icedwater

Reputation: 4887

Inspired by the preceding answers, this list comprehension looks at characters in b where corresponding characters in a exist, and returns their index i if those positions are not equal.

a = "CATCGTCCT"
b = "CACCGACCG"

mismatch = [i for i in range(0, len(a)) if a[i] != b[i]]

for pos in mismatch:
    print "At position", pos, "a had", a[pos], "while b had", b[pos], "."

Equivalent loop code for mismatch would be, as in this answer:

for i in range(0, len(a)):
    if a[i] != b[i]:
        mismatch.append(i)

Upvotes: 1

Tetsudou
Tetsudou

Reputation: 224

Just do:

a="CATCGTCCT"
b="CACCGACCG"
mismatch_seq=[]
for x in range (0, len(a)):
    if a[x] !=  b[x]:
        mismatch_seq.append(x)
print mismatch_seq

Upvotes: 1

user3666197
user3666197

Reputation: 1

A simplistic code may use this

a = "CATCGTCCT"                                             # SET a
b = "CACCGACCG"                                             # SET b

aListOfMismatchPOSITIONs = []                               # SET aList

for charPTR in range( len( a ) ):                           # LOOP over len( a )
    if  a[charPTR] != b[charPTR]:                           # .NE.
        aListOfMismatchPOSITIONs.append( charPTR)           #     APPEND
    else:                                                   # ELSE
        continue                                            #     LOOP^

print "A sequence of non-matching positions = ", aListOfMismatchPOSITIONs

Upvotes: 0

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