How to get the gap/mismatch positions of alignment

[leon945945]

Hi, as the title descripts, can biopython get the gap/mismatch positions of alignment, I didn't find a function to implement it.

[leon945945]

Hi, maybe I find how to get the mismatch position.
A for-loop will solve the problem.

def get_mis_pos(align):
    pos = []
    for i in range(align.get_alignment_length()):
        if align[0][i]!=align[1][i] and align[0][i]!="-" and align[1][i]!="-":
            pos.append(i)
    return pos 

[peterjc]

You didn't make it clear which kind of alignments in Biopython you were talking about, but perhaps the multiple sequence alignment object's counts method added in #4221 is what you want?