1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
|
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Utility functions for working with FDist (DEPRECATED)."""
from Bio.PopGen.GenePop import FileParser
import Bio.PopGen.FDist
# Quite a few utility functions could be done (like remove pop,
# add locus, etc...). The recommended strategy is convert back
# and forth from/to GenePop and use GenePop Utils
def convert_genepop_to_fdist(gp_rec, report_pops=None):
"""Converts a GenePop record to a FDist one.
Parameters:
gp_rec - Genepop Record (either standard or big)
Returns:
FDist record.
"""
if hasattr(gp_rec, "populations"):
return _convert_genepop_to_fdist(gp_rec)
else:
return _convert_genepop_to_fdist_big(gp_rec, report_pops)
def _convert_genepop_to_fdist(gp_rec):
"""Converts a standard GenePop record to a FDist one.
Parameters:
gp_rec - Genepop Record (Standard)
Returns:
FDist record.
"""
fd_rec = Bio.PopGen.FDist.Record()
fd_rec.data_org = 0
fd_rec.num_loci = len(gp_rec.loci_list)
fd_rec.num_pops = len(gp_rec.populations)
for lc_i in range(len(gp_rec.loci_list)):
alleles = []
pop_data = []
for pop_i in range(len(gp_rec.populations)):
for indiv in gp_rec.populations[pop_i]:
for al in indiv[1][lc_i]:
if al is not None and al not in alleles:
alleles.append(al)
alleles.sort() # Dominance requires this
# here we go again (necessary...)
for pop_i in range(len(gp_rec.populations)):
allele_counts = {}
for indiv in gp_rec.populations[pop_i]:
for al in indiv[1][lc_i]:
if al is not None:
count = allele_counts.get(al, 0)
allele_counts[al] = count + 1
allele_array = [] # We need the same order as in alleles
for allele in alleles:
allele_array.append(allele_counts.get(allele, 0))
pop_data.append(allele_array)
fd_rec.loci_data.append((len(alleles), pop_data))
return fd_rec
def _convert_genepop_to_fdist_big(gp_rec, report_pops=None):
"""Converts a big GenePop record to a FDist one.
Parameters:
gp_rec - Genepop Record (Big)
Returns:
FDist record.
"""
fd_rec = Bio.PopGen.FDist.Record()
fd_rec.data_org = 1
fd_rec.num_loci = len(gp_rec.loci_list)
num_loci = len(gp_rec.loci_list)
loci = []
for i in range(num_loci):
loci.append(set())
pops = []
work_rec = FileParser.read(gp_rec.fname)
lParser = work_rec.get_individual()
def init_pop():
my_pop = []
for i in range(num_loci):
my_pop.append({})
return my_pop
curr_pop = init_pop()
num_pops = 1
if report_pops:
report_pops(num_pops)
while lParser:
if lParser is not True:
for loci_pos in range(num_loci):
for al in lParser[1][loci_pos]:
if al is not None:
loci[loci_pos].add(al)
curr_pop[loci_pos][al] = curr_pop[loci_pos].get(al, 0) + 1
else:
pops.append(curr_pop)
num_pops += 1
if report_pops:
report_pops(num_pops)
curr_pop = init_pop()
lParser = work_rec.get_individual()
work_rec._handle.close() # TODO - Needs a proper fix
pops.append(curr_pop)
fd_rec.num_pops = num_pops
for loci_pos in range(num_loci):
alleles = sorted(loci[loci_pos])
loci_rec = [len(alleles), []]
for pop in pops:
pop_rec = []
for allele in alleles:
pop_rec.append(pop[loci_pos].get(allele, 0))
loci_rec[1].append(pop_rec)
fd_rec.loci_data.append(tuple(loci_rec))
return fd_rec
def _convert_genepop_to_fdist_big_old(gp_rec, report_loci=None):
"""Converts a big GenePop record to a FDist one.
Parameters:
gp_rec - Genepop Record (Big)
Returns:
FDist record.
"""
fd_rec = Bio.PopGen.FDist.Record()
def countPops(rec):
f2 = FileParser.read(rec.fname)
popCnt = 1
while f2.skip_population():
popCnt += 1
return popCnt
fd_rec.data_org = 0
fd_rec.num_loci = len(gp_rec.loci_list)
work_rec0 = FileParser.read(gp_rec.fname)
fd_rec.num_pops = countPops(work_rec0)
num_loci = len(gp_rec.loci_list)
for lc_i in range(num_loci):
if report_loci:
report_loci(lc_i, num_loci)
work_rec = FileParser.read(gp_rec.fname)
work_rec2 = FileParser.read(gp_rec.fname)
alleles = []
pop_data = []
lParser = work_rec.get_individual()
while lParser:
if lParser is not True:
for al in lParser[1][lc_i]:
if al is not None and al not in alleles:
alleles.append(al)
lParser = work_rec.get_individual()
# here we go again (necessary...)
alleles.sort()
def process_pop(pop_data, alleles, allele_counts):
allele_array = [] # We need the same order as in alleles
for allele in alleles:
allele_array.append(allele_counts.get(allele, 0))
pop_data.append(allele_array)
lParser = work_rec2.get_individual()
allele_counts = {}
for allele in alleles:
allele_counts[allele] = 0
allele_counts[None] = 0
while lParser:
if lParser is True:
process_pop(pop_data, alleles, allele_counts)
allele_counts = {}
for allele in alleles:
allele_counts[allele] = 0
allele_counts[None] = 0
else:
for al in lParser[1][lc_i]:
allele_counts[al] += 1
lParser = work_rec2.get_individual()
process_pop(pop_data, alleles, allele_counts)
fd_rec.loci_data.append((len(alleles), pop_data))
return fd_rec
def approximate_fst(desired_fst, simulated_fst, parameter_fst,
max_run_fst=1, min_run_fst=0, limit=0.005):
"""Calculates the next Fst attempt in order to approximate a
desired Fst.
"""
if abs(simulated_fst - desired_fst) < limit:
return parameter_fst, max_run_fst, min_run_fst
if simulated_fst > desired_fst:
max_run_fst = parameter_fst
next_parameter_fst = (min_run_fst + parameter_fst) / 2
else:
min_run_fst = parameter_fst
next_parameter_fst = (max_run_fst + parameter_fst) / 2
return next_parameter_fst, max_run_fst, min_run_fst
|
