Printing a non concordant position within a string

Question

I am writing a program that analyzes and parses consensus sequences. I have successfully gotten the analyzing and parsing to work and the program tells me whether two sequences are concordant or not.

I want to add an additional feature, if the two sequences are not concordant, I want it to tell me the position where the two sequences do not match up.

For example:

If sequence 1 is: GACTTTTTACTTTTTTG & sequence 2 is: GACCTTTTACTTTTTTG

it will tell me sequence 1 is not concordant to sequence 2, but I also want it to tell me the position of the non concordance is the 4th letter.

How can I get the program to do this?

Here is the code I have so far:

for (h1,s1),(h2,s2) in combinations(zip(header,sequence),2):
    if s1[start:stop]==s2[start:stop]:
        print h1, "is concordant to", h2
    else:
        print h1, "is not concordant to", h2
        nonconcordance_position=[]
        nonconcordance_position.append(idx2[n-1])
        print "position of non concordance:", nonconcordance_position

When I run this it works, however it does not give the correct position.

If concordance means whether the strings are exactly the same, then this is the same as finding the common prefix of two strings. If so, http://stackoverflow.com/a/6718435/85337 is a good way to do that. Specifically using `os.path.commonprefix`. — Justin Anderson, Aug 11 '16 at 15:44

Kory Schneider · Answer 1 · 2016-08-11T15:42:24.113

0

In your else statement you could loop through the sequence string and then print the index when the characters don't match.

Something like:

else:
    for i in range(0, len(h1)):
        if h1[i] == h2[i]:
            continue
        else:
            print i
            break

edited Aug 11 '16 at 15:42

answered Aug 11 '16 at 15:37

Kory Schneider

1
3

how can I do that? – Gia Constantina Aug 11 '16 at 15:38

Printing a non concordant position within a string

1 Answers1