示例#1
0
def find_min_vdel(v_nt, cdr3_aa):
    # find the minimum number of V nucleotides need to be deleted to
    # result in the CDR3aa
    v_aa = lcommon.nt2aa(v_nt)
    matchseq = left_max_match(v_aa, cdr3_aa)  # max matched aa seq
    len_ntmatch = len(matchseq) * 3
    min_vdel = len(v_nt) - len_ntmatch
    # see if 1 or 2 of the next v nts can result in the next cdr3 aa
    if min_vdel > 0 and len(cdr3_aa) > len(matchseq):
        if min_vdel >= 2:
            v_nts = v_nt[len_ntmatch: len_ntmatch + 2]
        else:
            v_nts = v_nt[len_ntmatch]
        
        got2nts = False
        firstaa = cdr3_aa[len(matchseq)]
        codons = lcommon.aa2codons(firstaa)
        for codon in codons:
            if re.match(v_nts, codon):
                min_vdel -= len(v_nts)
                got2nts = True
                break
        if len(v_nts) == 2 and not got2nts:
            for codon in codons:
                if re.match(v_nts[0], codon):
                    min_vdel -= 1
                    break
    return min_vdel
示例#2
0
def find_min_jdel(j_nt, cdr3_aa):
    # find the minimum number of J nucleotides need to be deleted to
    # result in the CDR3aa
    hang_j = len(j_nt) % 3
    hang_j_nts = j_nt[: hang_j]  # the 5' of j nt seq that not part of a codon
    
    j_aa = lcommon.nt2aa(j_nt[hang_j:])
    matchseq = right_max_match(j_aa, cdr3_aa)
    len_ntmatch = len(matchseq) * 3
    min_jdel = len(j_nt) - len_ntmatch
    if min_jdel > 0 and len(cdr3_aa) > len(matchseq):
        if min_jdel >= 2:
            j_nts = j_nt[min_jdel - 2: min_jdel]
        else:
            j_nts = j_nt[min_jdel - 1]
        
        got2nts = False
        firstaa = cdr3_aa[len(cdr3_aa) - len(matchseq) - 1]
        codons = lcommon.aa2codons(firstaa)
        for codon in codons:
            if codon[-1 * len(j_nts): ] == j_nts:
                min_jdel -= len(j_nts)
                got2nts = True
                break
        if len(j_nts) == 2 and not got2nts:
            for codon in codons:
                if codon[2] == j_nts[1]:
                    min_jdel -= 1
                    break
    return min_jdel
示例#3
0
def get_all_codons(aaseq):
    codon_lists = []
    for aa in aaseq:
        codon_lists.append(lcommon.aa2codons(aa))
    return codon_lists