def mktest(codon_alns, codon_table=default_codon_table, alpha=0.05):
"""McDonald-Kreitman test for neutrality (PMID: 1904993) This method
counts changes rather than sites (http://mkt.uab.es/mkt/help_mkt.asp).
Arguments:
- codon_alns - list of CodonAlignment to compare (each
CodonAlignment object corresponds to gene
sampled from a species)
Return the p-value of test result
"""
import copy
if not all(isinstance(i, CodonAlignment) for i in codon_alns):
raise TypeError("mktest accepts CodonAlignment list.")
codon_aln_len = [i.get_alignment_length() for i in codon_alns]
if len(set(codon_aln_len)) != 1:
raise RuntimeError("CodonAlignment object for mktest should be of"
" equal length.")
codon_num = codon_aln_len[0] // 3
# prepare codon_dict (taking stop codon as an extra amino acid)
codon_dict = copy.deepcopy(codon_table.forward_table)
for stop in codon_table.stop_codons:
codon_dict[stop] = 'stop'
# prepare codon_lst
codon_lst = []
for codon_aln in codon_alns:
codon_lst.append([])
for i in codon_aln:
codon_lst[-1].append(_get_codon_list(i.seq))
codon_set = []
for i in range(codon_num):
uniq_codons = []
for j in codon_lst:
uniq_codon = set(k[i] for k in j)
uniq_codons.append(uniq_codon)
codon_set.append(uniq_codons)
syn_fix, nonsyn_fix, syn_poly, nonsyn_poly = 0, 0, 0, 0
G, nonsyn_G = _get_codon2codon_matrix(codon_table=codon_table)
for i in codon_set:
all_codon = i[0].union(*i[1:])
if '-' in all_codon or len(all_codon) == 1:
continue
fix_or_not = all(len(k) == 1 for k in i)
if fix_or_not:
# fixed
nonsyn_subgraph = _get_subgraph(all_codon, nonsyn_G)
subgraph = _get_subgraph(all_codon, G)
this_non = _count_replacement(all_codon, nonsyn_subgraph)
this_syn = _count_replacement(all_codon, subgraph) - this_non
nonsyn_fix += this_non
syn_fix += this_syn
else:
# not fixed
nonsyn_subgraph = _get_subgraph(all_codon, nonsyn_G)
subgraph = _get_subgraph(all_codon, G)
this_non = _count_replacement(all_codon, nonsyn_subgraph)
this_syn = _count_replacement(all_codon, subgraph) - this_non
nonsyn_poly += this_non
syn_poly += this_syn
return _G_test([syn_fix, nonsyn_fix, syn_poly, nonsyn_poly])
def mktest(codon_alns, codon_table=default_codon_table, alpha=0.05):
"""McDonald-Kreitman test for neutrality (PMID: 1904993) This method
counts changes rather than sites (http://mkt.uab.es/mkt/help_mkt.asp).
Arguments:
- codon_alns - list of CodonAlignment to compare (each
CodonAlignment object corresponds to gene
sampled from a species)
Return the p-value of test result
"""
import copy
if not all([isinstance(i, CodonAlignment) for i in codon_alns]):
raise TypeError("mktest accepts CodonAlignment list.")
codon_aln_len = [i.get_alignment_length() for i in codon_alns]
if len(set(codon_aln_len)) != 1:
raise RuntimeError("CodonAlignment object for mktest should be of"
" equal length.")
codon_num = codon_aln_len[0] // 3
# prepare codon_dict (taking stop codon as an extra amino acid)
codon_dict = copy.deepcopy(codon_table.forward_table)
for stop in codon_table.stop_codons:
codon_dict[stop] = 'stop'
# prepare codon_lst
codon_lst = []
for codon_aln in codon_alns:
codon_lst.append([])
for i in codon_aln:
codon_lst[-1].append(_get_codon_list(i.seq))
codon_set = []
for i in range(codon_num):
uniq_codons = []
for j in codon_lst:
uniq_codon = set([k[i] for k in j])
uniq_codons.append(uniq_codon)
codon_set.append(uniq_codons)
syn_fix, nonsyn_fix, syn_poly, nonsyn_poly = 0, 0, 0, 0
G, nonsyn_G = _get_codon2codon_matrix(codon_table=codon_table)
for i in codon_set:
all_codon = i[0].union(*i[1:])
if '-' in all_codon or len(all_codon) == 1:
continue
fix_or_not = all([len(k) == 1 for k in i])
if fix_or_not:
# fixed
nonsyn_subgraph = _get_subgraph(all_codon, nonsyn_G)
subgraph = _get_subgraph(all_codon, G)
this_non = _count_replacement(all_codon, nonsyn_subgraph)
this_syn = _count_replacement(all_codon, subgraph) - this_non
nonsyn_fix += this_non
syn_fix += this_syn
else:
# not fixed
nonsyn_subgraph = _get_subgraph(all_codon, nonsyn_G)
subgraph = _get_subgraph(all_codon, G)
this_non = _count_replacement(all_codon, nonsyn_subgraph)
this_syn = _count_replacement(all_codon, subgraph) - this_non
nonsyn_poly += this_non
syn_poly += this_syn
return _G_test([syn_fix, nonsyn_fix, syn_poly, nonsyn_poly])
