This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Overlap between Genome and Pattern

Hello everyone, I am trying to implement this method but failed to have the output answer. Can someone help me take a look what I could be missing? So basically, we have a string Genome, a Pattern, and integer of Overlap. We need to find number of matching occurrences of Pattern in Genome but with at most number of overlap. So the overlap between the Pattern can only be <= number of overlap to count.

I have attached the sample input and output, which is 2 but I lost at how to check for overlap within the string. Thank you for the feedback!

def PatternCountOverlap(Text, Pattern, overlap):
    n = len(Text)
    k = len(Pattern)
    count = 0
    for i in range(n-k+1): #iterate through the text 
        if Pattern == Text[i:i+k]:
            count +=1  #count number of matching 
            ##how to find with restriction of overlapping? 

    return count

print(PatternCountOverlap("GATATATATAC","ATATA",1))  #this would return 2, 1 is number of overlap restriction
overlap python pattern
• 1,943 views • link
updated by GenoMax GenoMax • written by kristenammons2 • kristenammons2

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

code_formatting

• 0 views • link
written by Ram Ram

Also, there is no need for the bioinformatics tag (I've removed it) - every question on the site is related to bioinformatics.

• 0 views • link
written by Ram Ram

kristenammons2 : Please do not delete posts once they have received an answer or a comment. If the answer below solved your problem then accept it (green check mark) to provide closure for this thread.

• 0 views • link
written by GenoMax GenoMax

1 answer

Try replacing return count with

if count <= overlap:
    return count
else:
    return overlap
• 0 views • link
updated by Ram Ram • written by Jeremy • Jeremy

I prefer ternary operators:

ret_val = count if count <= overlap else overlap #assign to a variable to make debugging easier
return ret_val
• 0 views • link
written by Ram Ram

Log in to answer this question.

More posts like this