def cook_constants_SizeChange(fasta_dict,
s1=1092,
NeC=2e5,
Nef=4e5,
Grate=1.03,
dir_data="./data/",
dir_vcf="vcf_data/sims/",
slim_dir='./',
batch_name=''):
'''
set up conditions.
constants:
- vcf_file;
- fasta_file - writes fasta; mkdir fasta_dir
- sampling:
s1 (int) to vary in range=nrange as proportion of Nmax;
- NeC: initial population eff. size.
- Nef: effective population size after change.
- Grate: growth rate during change.
'''
cookID = 'sizeChange'
sim_store = {}
for chrom in fasta_dict.keys():
for start in fasta_dict[chrom].keys():
fasta = fasta_dict[chrom][start]
### set up names and directories.
SIMname = batch_name + 'C{}.{}'.format(chrom, str(start))
SIM_dir = dir_data + SIMname
os.makedirs(SIM_dir, exist_ok=True)
vcf_file = SIM_dir + '/' + SIMname + "_chr{}.vcf".format(chrom)
#ref_dir= SIM_dir + SIMname + '_reference'
### write fasta file for SLiM.
fasta_file = write_fastaEx(fasta,
chrom=chrom,
start=start,
ID=SIMname,
fasta_dir=SIM_dir)
sim_store[SIMname] = {
"vcf_file": vcf_file,
"fasta_file": fasta_file,
"s1": s1,
"NeC": NeC,
"Nef": Nef,
"Grate": Grate,
}
### write arguments to file
write_args(sim_store[SIMname], SIMname, SIM_dir)
### population identifiers file
sample_sizes = [sim_store[SIMname][x] for x in ["s1"]]
write_popIDs(sample_sizes, file_dir=SIM_dir)
return sim_store, cookID
def cook_constants_Gravel2sampleRange(fasta_dict, nrange= [.05,.5], step= 10,
Nmax= 100, dir_data= "./data/", dir_vcf= "vcf_data/sims/",
slim_dir= './', batch_name= ''):
'''
set up conditions.
constants:
- vcf_file;
- fasta_file - writes fasta; mkdir fasta_dir
- sampling:
s1 (int) to vary in range=nrange as proportion of Nmax;
s2= Nmax - s1;
s3= 0
'''
cookID= 'Gravel2sampleRange'
sim_store= {}
s1range= np.linspace(nrange[0],nrange[1],step) * Nmax
s1range= np.array(s1range,dtype=int)
s2range= Nmax - s1range
s3= 0
d= 0
for chrom in fasta_dict.keys():
for start in fasta_dict[chrom].keys():
fasta= fasta_dict[chrom][start]
### set up names and directories.
SIMname= batch_name + 'C{}.{}'.format(chrom,str(start))
SIM_dir= dir_data + SIMname
os.makedirs(SIM_dir, exist_ok=True)
vcf_file= SIM_dir + '/' + SIMname + "_chr{}.vcf".format(chrom)
#ref_dir= SIM_dir + SIMname + '_reference'
### write fasta file for SLiM.
fasta_file= write_fastaEx(fasta,chrom=chrom,start= start,
ID= SIMname,fasta_dir= SIM_dir)
sim_store[SIMname]= {
"vcf_file": vcf_file,
"fasta_file": fasta_file,
"s1": s1range[d],
"s2": s2range[d],
"s3": s3
}
### write arguments to file
write_args(sim_store[SIMname],SIMname,SIM_dir)
### population identifiers file
sample_sizes= [sim_store[SIMname][x] for x in ["s1","s2","s3"]]
write_popIDs(sample_sizes,file_dir= SIM_dir)
d += 1
return sim_store, cookID
def cook_constants_v1(fasta_dict,
s1=216,
s2=108,
s3=206,
dir_data="./data/sims/",
dir_vcf="vcf_data/",
slim_dir='./',
batch_name=''):
'''
set up conditions.
constants:
- vcf_file;
- fasta_file - writes fasta; mkdir fasta_dir
- sampling: s1= 216;s2=108;s3=206
'''
cookID = 'v1'
sim_store = {}
for chrom in fasta_dict.keys():
for start in fasta_dict[chrom].keys():
fasta = fasta_dict[chrom][start]
### set up names and directories.
SIMname = batch_name + 'C{}.{}'.format(chrom, str(start))
SIM_dir = dir_data + SIMname + '/'
os.makedirs(SIM_dir, exist_ok=True)
vcf_file = SIM_dir + SIMname + "_chr{}.vcf".format(chrom)
#ref_dir= SIM_dir + SIMname + '_reference'
### write fasta file for SLiM.
fasta_file = write_fastaEx(fasta,
chrom=chrom,
start=start,
ID=SIMname,
fasta_dir=SIM_dir)
sim_store[SIMname] = {
"vcf_file": vcf_file,
"fasta_file": fasta_file,
"s1": s1,
"s2": s2,
"s3": s3
}
### write arguments to file
write_args(sim_store[SIMname], SIMname, SIM_dir)
### population identifiers file
sample_sizes = [sim_store[SIMname][x] for x in ["s1", "s2", "s3"]]
write_popIDs(sample_sizes, file_dir=SIM_dir)
return sim_store, cookID
def cook_constants_ABC_ratevar(fasta_dict,
demo_file='Prado&Martinez2013_M4A.txt',
template='template_simple.slim',
mut_file='M4AM0_grid.txt',
Nsamp=5,
anc_r='0',
sizes=500,
burnin=5e4,
mu=1e-8,
rec=1e-8,
bases='ACGT',
rate_change=10,
rate_range=[1, 2],
Nmat=1,
sim_scale=1,
dir_data="./data/",
dir_vcf="vcf_data/sims/",
slim_dir='./',
batch_name=''):
'''
cookbook ABC_ratevar takes a mutation skew file (arg: mut_file) instead of generating them.
'''
from tools.ABC_utilities import demo_to_recipe
'''
set up conditions.
constants:
- vcf_file;
- fasta_file - writes fasta; mkdir fasta_dir
- sampling:
s1 (int) to vary in range=nrange as proportion of Nmax;
- NeC: initial population eff. size.
- Nef: effective population size after change.
- Grate: growth rate during change.
'''
cookID = 'ABCdemo'
recipe_dir = '/'.join(template.split('/')[:-1])
sim_store = {}
for chrom in fasta_dict.keys():
for start in fasta_dict[chrom].keys():
fasta = fasta_dict[chrom][start]
## create sim recipes from template
pops, files = demo_to_recipe(demo_file,
template,
batch=batch_name,
anc_r=anc_r,
Nsamp=Nsamp,
recipe_dir=recipe_dir,
sim_scale=sim_scale)
for idx in range(Nsamp):
### set up names and directories.
SIMname = batch_name + 'C{}.{}.{}'.format(
chrom, str(start), idx)
SIM_dir = dir_data + SIMname
recipe = files[idx]
os.makedirs(SIM_dir, exist_ok=True)
vcf_file = SIM_dir + '/' + SIMname + "_chr{}.vcf".format(chrom)
#ref_dir= SIM_dir + SIMname + '_reference'
### write fasta file for SLiM.
fasta_file = write_fastaEx(fasta,
chrom=chrom,
start=start,
ID=SIMname,
fasta_dir=SIM_dir)
rec_here = rec / [1, sim_scale][int(rec != 0.5)]
sim_store[SIMname] = {
"vcf_file": vcf_file,
"fasta_file": fasta_file,
"mu": mu / sim_scale,
"mut_file": mut_file,
'recipe': recipe,
'rec': rec_here
}
pop_dict = {x: sizes for x in pops}
#sim_store[SIMname].update(pop_dict)
### write arguments to file
write_args(sim_store[SIMname], SIMname, SIM_dir)
### population identifiers file
sample_sizes = [pop_dict[x] for x in pop_dict.keys()]
write_popIDs(sample_sizes, file_dir=SIM_dir)
return sim_store, cookID
def cook_constants_ABC(fasta_dict,
demo_file='Prado&Martinez2013_M4A.txt',
template='template_simple.slim',
Nsamp=5,
anc_r='0',
sizes=500,
burnin=5e4,
mu=1e-8,
rec=1e-8,
bases='ACGT',
rate_change=10,
rate_range=[1, 5],
Nmat=0,
sim_scale=1,
dir_data="./data/",
dir_vcf="vcf_data/sims/",
slim_dir='./',
batch_name=''):
from tools.ABC_utilities import demo_to_recipe
'''
set up conditions.
constants:
- vcf_file;
- fasta_file - writes fasta; mkdir fasta_dir
- sampling:
s1 (int) to vary in range=nrange as proportion of Nmax;
- NeC: initial population eff. size.
- Nef: effective population size after change.
- Grate: growth rate during change.
'''
cookID = 'ABCdemo'
recipe_dir = '/'.join(template.split('/')[:-1])
sim_store = {}
mutations_full_dict, mutations_full_list, mut_org = mutation_dict_full(
bases=bases)
var_store = {
"M{}".format(x): rate_mods(mut_org,
rate_range=rate_range,
rate_change=rate_change,
bases=bases,
mu=mu)
for x in range(1, Nmat + 1)
}
var_store["M0"] = {}
mat_names = {
mat: batch_name + mat + '_grid.txt'
for mat in var_store.keys()
}
for mat in var_store.keys():
with open(mat_names[mat], 'w') as fp:
for mut in var_store[mat].keys():
rates = var_store[mat][mut]
rates = ','.join([str(x) for x in rates])
fp.write('\t'.join([mut, rates]) + '\n')
for chrom in fasta_dict.keys():
for start in fasta_dict[chrom].keys():
fasta = fasta_dict[chrom][start]
for mat in var_store.keys():
## create sim recipes from template
pops, files = demo_to_recipe(demo_file,
template,
batch=batch_name,
anc_r=anc_r,
Nsamp=Nsamp,
recipe_dir=recipe_dir,
sim_scale=sim_scale)
for idx in range(Nsamp):
### set up names and directories.
SIMname = batch_name + mat + 's' + str(
idx) + 'C{}.{}'.format(chrom, str(start))
SIM_dir = dir_data + SIMname
recipe = files[idx]
os.makedirs(SIM_dir, exist_ok=True)
vcf_file = SIM_dir + '/' + SIMname + "_chr{}.vcf".format(
chrom)
#ref_dir= SIM_dir + SIMname + '_reference'
### write fasta file for SLiM.
fasta_file = write_fastaEx(fasta,
chrom=chrom,
start=start,
ID=SIMname,
fasta_dir=SIM_dir)
rec_here = rec / [1, sim_scale][int(rec != 0.5)]
sim_store[SIMname] = {
"vcf_file": vcf_file,
"fasta_file": fasta_file,
"mu": mu,
"rec": rec_here,
"mut_file": mat_names[mat],
'recipe': recipe
}
pop_dict = {x: sizes for x in pops}
#sim_store[SIMname].update(pop_dict)
### write arguments to file
write_args(sim_store[SIMname], SIMname, SIM_dir)
### population identifiers file
sample_sizes = [pop_dict[x] for x in pop_dict.keys()]
write_popIDs(sample_sizes, file_dir=SIM_dir)
return sim_store, cookID
def cook_constants_rateVarMat(fasta_dict,
mu=1e-8,
bases='ACGT',
rate_change=10,
rate_range=[1, 5],
Nmat=5,
s1=2000,
NeC=2e5,
Nef=4e5,
Grate=1.03,
dir_data="./data/",
dir_vcf="vcf_data/sims/",
slim_dir='./',
batch_name=''):
'''
set up conditions.
constants:
- vcf_file;
- fasta_file - writes fasta; mkdir fasta_dir
- sampling:
s1 (int) to vary in range=nrange as proportion of Nmax;
- NeC: initial population eff. size.
- Nef: effective population size after change.
- Grate: growth rate during change.
'''
cookID = 'rateVarII'
sim_store = {}
mutations_full_dict, mutations_full_list, mut_org = mutation_dict_full(
bases=bases)
var_store = {
"M{}".format(x): rate_mods(mut_org,
rate_range=rate_range,
rate_change=rate_change,
bases=bases,
mu=mu)
for x in range(1, Nmat + 1)
}
var_store["M0"] = {}
mat_names = {
mat: batch_name + mat + '_grid.txt'
for mat in var_store.keys()
}
for mat in var_store.keys():
with open(mat_names[mat], 'w') as fp:
for mut in var_store[mat].keys():
rates = var_store[mat][mut]
rates = ','.join([str(x) for x in rates])
fp.write('\t'.join([mut, rates]) + '\n')
for chrom in fasta_dict.keys():
for start in fasta_dict[chrom].keys():
fasta = fasta_dict[chrom][start]
for mat in var_store.keys():
### set up names and directories.
SIMname = batch_name + mat + 'C{}.{}'.format(chrom, str(start))
SIM_dir = dir_data + SIMname
os.makedirs(SIM_dir, exist_ok=True)
vcf_file = SIM_dir + '/' + SIMname + "_chr{}.vcf".format(chrom)
#ref_dir= SIM_dir + SIMname + '_reference'
### write fasta file for SLiM.
fasta_file = write_fastaEx(fasta,
chrom=chrom,
start=start,
ID=SIMname,
fasta_dir=SIM_dir)
sim_store[SIMname] = {
"vcf_file": vcf_file,
"fasta_file": fasta_file,
"s1": s1,
"NeC": NeC,
"Nef": Nef,
"Grate": Grate,
"mu": mu,
"mut_file": mat_names[mat]
#"other": {'//mut_file': '\tfile_mut= readFile("{}");\n'.format(mut_file)}
}
### write arguments to file
write_args(sim_store[SIMname], SIMname, SIM_dir)
### population identifiers file
sample_sizes = [sim_store[SIMname][x] for x in ["s1"]]
write_popIDs(sample_sizes, file_dir=SIM_dir)
return sim_store, cookID
def cook_constants_Burnin(fasta_dict,
bt=50000,
sdelay=1000,
s1=1092,
NeC=2e5,
Nef=4e5,
Grate=1.03,
dir_data="./data/",
dir_vcf="vcf_data/sims/",
slim_dir='./',
batch_name=''):
'''
set up conditions.
constants:
- vcf_file;
- fasta_file - writes fasta; mkdir fasta_dir
- sampling:
s1 (int) to vary in range=nrange as proportion of Nmax;
- NeC: initial population eff. size.
- Nef: effective population size after change.
- Grate: growth rate during change.
'''
cookID = 'burnin'
sim_store = {}
possible = sum([len(fasta_dict[x]) for x in fasta_dict.keys()])
burnin_list = np.linspace(1, bt, possible, dtype=int)
d = 0
for chrom in fasta_dict.keys():
for start in fasta_dict[chrom].keys():
fasta = fasta_dict[chrom][start]
# burnin time
evt = burnin_list[d]
st = burnin_list[d] + sdelay
### set up names and directories.
SIMname = batch_name + 'T{}'.format(evt) + 'C{}.{}'.format(
chrom, str(start))
SIM_dir = dir_data + SIMname
os.makedirs(SIM_dir, exist_ok=True)
vcf_file = SIM_dir + '/' + SIMname + "_chr{}.vcf".format(chrom)
#ref_dir= SIM_dir + SIMname + '_reference'
### write fasta file for SLiM.
fasta_file = write_fastaEx(fasta,
chrom=chrom,
start=start,
ID=SIMname,
fasta_dir=SIM_dir)
sim_store[SIMname] = {
"vcf_file": vcf_file,
"fasta_file": fasta_file,
"s1": s1,
"NeC": NeC,
"Nef": Nef,
"Grate": Grate,
"evt": evt,
"other": {
"//grow": "{}: ".format(evt) + "{\n",
"//sample": "{} late() ".format(st) + "{\n"
}
}
### write arguments to file
write_args(sim_store[SIMname], SIMname, SIM_dir)
### population identifiers file
sample_sizes = [sim_store[SIMname][x] for x in ["s1"]]
write_popIDs(sample_sizes, file_dir=SIM_dir)
d += 1
return sim_store, cookID
