Pairwise Comparison Of DNA Sequences function- stuck and cant find why

[pwolf]

The exercise says the following:
"""
Pairwise comparision of DNA sequences is a popular technique used in Bioinformatics. It usually involves some scoring scheme to express the degree of similarity. Write a function that compares two DNA sequences based on the following scoring scheme: +1 for a match, +3 for each consecutive match and -1 for each mismatch.

Examples

>>> print pairwiseScore("ATTCGT", "ATCTAT")
    ATTCGT
    ||   |
    ATCTAT
    Score: 2 
    >>> print pairwiseScore("GATAAATCTGGTCT", "CATTCATCATGCAA")
    GATAAATCTGGTCT
     ||  |||  |   
    CATTCATCATGCAA
    Score: 4 
    >>>

"""
so i wrote the following, which was continuously working until i started playing with it, now i cant find whats wrong with it! please help me by pointing out where i went wrong?

def pariwiseScore(seqA, seqB):
	h = []
	c = []
	for x in range(0,len(seqA)):
		if seqA[x] == seqB[x]:
			h.append('|')
		else:
			h.append(' ')
		if len(h) > 1:
			if h[x] == '|':
				try:
					if h[x] == h[x-1]:
						c.append(3)
				except IndexError:
					c.append(1)

			elif h[x] == ' ':
				c.append(-1)
		else:
			if h[x] == '|':
				c.append(1)
			elif h[x] == ' ':
				c.append(-1)
	a = "".join(h)
	return seqA, '\n', a, '\n', seqB, '\n', 'Score: %I' % sum(c)

Any help is much appreciated.

[pwolf]

P.s i had it before and it was returning the correct sum, but i copied it into a notepad and accidentally closed it. Now i cant get it working

[pwolf]

noticed my problem, renamed it to pariwise and was still testing for pairwise, also flawed format specifier

[pwolf]

its still not returning right, why is it that when i use print it works fine but when return and print the results of the function it wont?

def pairwiseScore(seqA, seqB):
	h = []
	c = []
	for x in range(0,len(seqA)):
		if seqA[x] == seqB[x]:
			h.append('|')
		else:
			h.append(' ')
		if len(h) > 1:
			if h[x] == '|':
				if h[x] == h[x-1]:
					c.append(3)
				else:
					c.append(1)
			elif h[x] == ' ':
				c.append(-1)
		else:
			if h[x] == '|':
				c.append(1)
			elif h[x] == ' ':
				c.append(-1)
	a = "".join(h)
	return seqA, '\n', a, '\n', seqB, '\n', 'Score: %d' % sum(c)

is my code and it results as follows:

>>> print pairwiseScore("ATTCGT", "ATCTAT")
('ATTCGT', '\n', '||   |', '\n', 'ATCTAT', '\n', 'Score: 2')

how can i remedy this?

[valorien]

It seems like you're returning a tuple and not a string.
try this and see what happens:

for item in pairwiseScore("ATTCGT", "ATCTAT"):
    print(item)

or maybe you could try returning str(return value) in the function itself.
Good Luck.

[Gribouillis]

Try

return "".join((seqA, '\n', a, '\n', seqB, '\n', 'Score: %d' % sum(c)))

edit: don't use tabs to indent python code, use 4 spaces.

[pwolf]

Try

return "".join((seqA, '\n', a, '\n', seqB, '\n', 'Score: %d' % sum(c)))

edit: don't use tabs to indent python code, use 4 spaces.

Thanks, very helpful! i wish i wasn't so bad at this stuff, usually im a fairly quick learner but i guess im just not suited to programming!

[turtletrader23]

Hi, I am having trouble with this exercise too. For some reason I can get this to work in console, but when I submit the answer to pyschool it doesn't work.

def pairwiseScore(seqA, seqB): 
    length = len(seqA)
    counter = 0
    sequence = ""
    score = 0
    while counter < 1:
        if seqA[counter] == seqB[counter]:
            sequence = sequence + "|"
            counter = counter + 1
            score = score + 1
    while counter < length:
        if seqA[counter] == seqB[counter] and sequence[-1] == "|":
            sequence = sequence + "|"
            counter = counter + 1
            score = score + 3
        elif seqA[counter] == seqB[counter] and sequence[-1] != "|":
            sequence = sequence + "|"
            counter = counter + 1
            score = score + 1    
        elif seqA[counter] != seqB[counter]:
            sequence = sequence + " "
            counter = counter + 1
            score = score - 1
    print "%s \n %s \n %s \nScore: %d" % (seqA, sequence, seqB, score)

[TrustyTony]

You seem to have spaces between the parts of answer, probably answer should be direct concatenation of parts.

[TrustyTony]

You are not returning value, so value of your function will be None, also the result does not correspond to the test print when I run the code, first test wrong and hangup for second.

ATTCGT
 ||   |
 ATCTAT
Score: 2
None

Here my little advanced way:

def pairwiseScore(seqA, seqB):
    matches = ''.join('|' if a==b else ' ' for a,b in zip(seqA, seqB))
    # count does not deal with overlapping matches so must use zip for two extra points for consecutive matches
    score = matches.count('|') - matches.count(' ') + 2 * sum( a==b=='|' for a,b in zip(matches, matches[1:]))
    return '\n'.join((seqA, matches, seqB, 'Score: %i' % score))

print(pairwiseScore("ATTCGT", "ATCTAT"))
print('')
print(pairwiseScore("GATAAATCTGGTCT", "CATTCATCATGCAA"))