Count how many gaps and mismatches using pairwise2 alignment
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2.1 years ago

I am doing a local alignment using pairwise2. I currently have some code that will count how many matches there are but I am trying to also count how many gaps and mismatches there are in the alignment too. Is there any way to do this? If possible I'd like the gaps and mismatches counted separately form each other and the position of the gaps/mismatches in the sequence would be super helpful.

alignment sequence • 1.8k views
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Entering edit mode

Could you please share what you've tried and what is your code ?

I assume you took python module pairwise2

You can take a look at the format_alignment function and rewrite your own, something like this

def my_format_alignment(align1, align2, score, begin, end): 
    s = [] 
    s.append("%s\n" % align1) 
    s.append(" " * begin) 
    gap=0
    mismatch=0
    for a, b in zip(align1[begin:end], align2[begin:end]): 
        if a == b: 
            s.append("|")  # match 
        elif a == "-" or b == "-": 
            s.append(" ")  # gap
            gap+=1
        else: 
            s.append(".")  # mismatch 
            mismatch+=1
    s.append("\n") 
    s.append("%s\n" % align2) 
    s.append("  Score=%g\n" % score)
    s.append("  Gap=%g\n" % gap)
    s.append("  Mismatch=%g\n" % mismatch)
    return ''.join(s) 

from Bio import pairwise2
alignments = pairwise2.align.globalxx("ACCGT", "ACG")
from Bio.pairwise2 import format_alignment
print(format_alignment(*alignments[0]))
#ACCGT
#| || 
#A-CG-
#  Score=3
print(my_format_alignment(*alignments[0]))
#ACCGT
#| || 
#A-CG-
#  Score=3
#  Gap=2
#  Mismatch=0
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