通过计算edist距离，如果小于3个碱基错配，则认为识别到引物。

import numpy as np

def reverse_complement(t):
    """反向互补序列"""
    completement = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C','N': 'N'}
    s = ''
    for base in t:
        s = completement[base] + s 
    return s
    
def edist(p,t):
    """
    p: primer
    t: target sequence
    calculate edist distance
    """
    p_len = len(p)
    t_len = len(t)
    data = np.zeros(shape=(p_len+1,t_len+1), dtype=int)
    
    # i for row(primer), j for col(target sequence)
    for i in range(p_len+1):
        data[i][0] = i

    # edist distance
    for i in range(1,p_len+1):
        for j in range(1,t_len+1): 
            hor = data[i][j-1] + 1  # horizontal
            ver = data[i-1][j] + 1  # vertical

            # diag
            if p[i-1] == t[j-1]:
                delta = 0
            else:
                delta = 1
            dia = data[i-1][j-1] + delta
            
            data[i][j] = min(ver, hor, dia)
    return(data, min(data[p_len]))    

def primer_align(p,t):
    """
    align a single primer to a sequence.
    t: target sequence
    """
    edist1, forward_dist1 = edist(p, t)
    edist2, forward_dist2 = edist(p, reverse_complement(t))
    if forward_dist1 < forward_dist2:
        return edist1, forward_dist1
    else:
        return edist2, forward_dist2

def primers_align(f, r, t, mismatch=3):
    """
    align a pair of primers to a sequence
    """

    # 1/3 region
    _, forward_dist = primer_align(f, t[:int(len(t)/3)])
    _, reverse_dist = primer_align(reverse_complement(r), t[int(len(t)/3*2):-1])
    if forward_dist <= mismatch or reverse_dist <= mismatch:
        return 'aligned'
    else:
        return 'unaligned'

if __name__ == '__main__':
    forward = 'ATCG'
    fa = 'ACTCA'
    print(edist(forward, fa))

(array([[0, 0, 0, 0, 0, 0],
       [1, 0, 1, 1, 1, 0],
       [2, 1, 1, 1, 2, 1],
       [3, 2, 1, 2, 1, 2],
       [4, 3, 2, 2, 2, 2]]), 2)