Newer
Older
email: ullrich@evolbio.mpg.de
License: MIT
The MIT License (MIT)
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
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
'''
import sys
import argparse
import numpy as np
import random as rnd
from Bio import Seq
from Bio import SeqIO
from Bio import SeqRecord
def duplicate_sequence(rec):
duplicated_seq = SeqRecord.SeqRecord(rec.seq.tomutable())
duplicated_seq.id = rec.id
duplicated_seq.name = rec.name
duplicated_seq.description = rec.description
return duplicated_seq
def mutate_pos(nuc):
if nuc in '.-NRYSWKMBDHV':
return [nuc, 0]
if nuc not in '.-NRYSWKMBDHV':
return [rnd.sample([x for x in ['A','T','C','G'] if x != nuc],1)[0], 1]
def change_random_pos(fasta_dict_, div_, chr_, po_, ps_):
if chr_ == 'true':
sample_len = []
all_changed_pos = []
changed_sites = 0
for k in fasta_dict_.keys():
k_changed_sites = 0
k_changed_pos = {}
k_sample_len = int(np.ceil(len(fasta_dict_[k])*div_))
print('%s Sample len: %s' % (k,str(k_sample_len)))
sample_len.append(k_sample_len)
i = 0
while i != k_sample_len and k_changed_sites != k_sample_len and len(k_changed_pos) != len(fasta_dict_[k]):
change_pos = rnd.randint(0,len(fasta_dict_[k])-1)
if k+'_'+str(change_pos) in k_changed_pos:
continue
if k+'_'+str(change_pos) not in k_changed_pos:
k_changed_pos[k+'_'+str(change_pos)] = 0
fasta_dict_[k].seq[change_pos], j = mutate_pos(fasta_dict_[k][change_pos])
k_changed_sites += j
i += j
if po_ == 'true' and j != 0:
if k_changed_sites%ps_ == 0 and k_changed_sites%(ps_*5) != 0:
sys.stderr.write('.')
if k_changed_sites%ps_ == 0 and k_changed_sites%(ps_*5) == 0:
sys.stderr.write('o')
all_changed_pos.append(k_changed_pos.keys())
changed_sites += k_changed_sites
return [sample_len, changed_sites, all_changed_pos]
if chr_ == 'false':
changed_sites = 0
all_changed_pos = []
k_changed_pos = {}
total_len = np.sum([len(fasta_dict_[x]) for x in fasta_dict_])
sample_len = int(np.ceil(total_len*div_))
print('Sample len: %s' % (str(sample_len)))
i = 0
while i != sample_len and changed_sites != sample_len and len(k_changed_pos) != total_len:
k = rnd.sample(fasta_dict_.keys(),1)[0]
change_pos = rnd.randint(0,len(fasta_dict_[k])-1)
if k+'_'+str(change_pos) in k_changed_pos:
continue
if k+'_'+str(change_pos) not in k_changed_pos:
k_changed_pos[k+'_'+str(change_pos)] = 0
fasta_dict_[k].seq[change_pos], j = mutate_pos(fasta_dict_[k][change_pos])
changed_sites += j
i += j
if po_ == 'true' and j != 0:
if changed_sites%ps_ == 0 and changed_sites%(ps_*5) != 0:
sys.stderr.write('.')
if changed_sites%ps_ == 0 and changed_sites%(ps_*5) == 0:
sys.stderr.write('o')
all_changed_pos.append(k_changed_pos.keys())
return [sample_len, changed_sites, all_changed_pos]
def main():
parser = parser = argparse.ArgumentParser(prog='simdiv', usage='%(prog)s [options]',
description = 'Takes a reference fasta file as input and produces divergent fasta file given a divergence procent cutoff.')
parser.add_argument('-i', help = 'input fasta file')
parser.add_argument('-o', help = 'output fasta file')
parser.add_argument('-d', help = 'specify divergence procent [default: 0.01]', type = float, default = 0.01)
parser.add_argument('-chr', help = 'specify if each chromosome should be sampled indivdually [default: false]', choices = ['true','false'], default = 'false')
parser.add_argument('-po', help='specify if progress should be printed based on changed sites processed [default: true]', choices = ['true','false'], default = 'true')
parser.add_argument('-ps', help='specify progress steps [default: 1e5]', default='1e5')
parser.add_argument('-v', '--verbose', help='increase output verbosity', action='store_true')
args = parser.parse_args()
if args.i is None:
parser.print_help()
sys.exit('\n#####\nExit program: Please specify fasta input file.')
original_fasta = SeqIO.parse(args.i, "fasta")
if args.o is None:
parser.print_help()
sys.exit('\n#####\nExit program: Please specify fasta output file.')
outfile = args.o
option_div = args.d
option_chr = args.chr
option_po = args.po
option_ps = int(float(args.ps))
print("command arguments used:")
print(args)
fasta_dict = {}
fasta_len = []
print('Start parsing reference fasta files')
for record in original_fasta:
fasta_dict[record.id] = duplicate_sequence(record)
fasta_len.append(len(record))
print('Finished parsing reference fasta files')
print('Start sampling')
sample_len, changed_sites, all_changed_pos = change_random_pos(fasta_dict, option_div, option_chr, option_po, option_ps)
print('Finished sampling')
print('Sampled sites: %s' % (str(sample_len)))
print('Changed sites: %s' % (str(changed_sites)))
if args.verbose:
print('All changed pos: %s' % (str(all_changed_pos)))
print('Start writing fasta output')
SeqIO.write(fasta_dict.values(), outfile, "fasta")
print('Finshed writing fasta output')
if __name__ == '__main__':
main()