def snp_sel_v_neu_anavar(snp_sfs, snp_m, n_sfs, n_m, constraint, bootstrap, n, c, dfe, out_stem, fold, degree, search):
anavar_path = '/shared/evolgen1/shared_data/program_files/sharc/'
anavar_cmd = '{path}anavar1.22 {ctl} {rslts} {log}'
for i in [0] + range(1, bootstrap+1):
# sort sfs
if i == 0:
sfs = snp_sfs
sfs_n = n_sfs
else:
sfs = resample_replace(snp_sfs)
sfs_n = resample_replace(n_sfs)
# convert to correct format for anavar
sfs = sfs2counts(sfs, n)
sfs_n = sfs2counts(sfs_n, n)
# sort file names
ctl_name = out_stem + '.rep{}.control.txt'.format(i)
result_name = out_stem + '.rep{}.results.txt'.format(i)
log_name = out_stem + '.rep{}.log.txt'.format(i)
# construct control file
sfs_m = {'selected_SNP': (sfs, snp_m),
'neutral_SNP': (sfs_n, n_m)}
ctl = an.SNPNeuSelControlFile()
ctl.set_alg_opts(search=search, alg='NLOPT_LD_SLSQP')
ctl.set_data(sfs_m, n, dfe=dfe, c=c,
gamma_r=(-5e5, 1e3), theta_r=(1e-10, 0.1), r_r=(0.01, 100),
snp_fold=fold)
if degree != 50:
ctl.set_dfe_optional_opts(degree=degree, optional=True)
ctl.set_constraint(constraint)
ctl_contents = ctl.construct()
with open(ctl_name, 'w') as control:
control.write(ctl_contents)
# call anavar
rep_cmd = anavar_cmd.format(path=anavar_path, ctl=ctl_name, rslts=result_name, log=log_name)
subprocess.call(rep_cmd, shell=True)
def sel_v_neu_anavar_nonsense(vcf, call, constraint, n, c, dfe, alg, nnoimp,
maximp, out_stem, search, degree, spread,
evolgen, prem_files):
"""
submits anavar jobs to cluster after writing required files etc
:param vcf: str
:param call: dict
:param constraint: str
:param n: int
:param c: int
:param dfe: str
:param alg: str
:param nnoimp: int
:param maximp: int
:param out_stem: str
:param search: int
:param degree: int
:param spread: int
:param evolgen: bool
:param prem_files: list
:return: None
"""
anavar_path = '/shared/evolgen1/shared_data/program_files/sharc/'
anavar_cmd = '{path}anavar1.22 {ctl} {rslts} {log} {seed}'
# sort file names
ctl_name = out_stem + '.control.txt'
# get nonsense data in
nonsense_dict = gather_chromo_prems(prem_files)
sel_sfs, sel_m = prem_freqs_call(nonsense_dict)
# make control file
sfs_data = prepare_nonsense_snp_sfs(vcf, call, n, sel_sfs, sel_m)
ctl = an.SNPNeuSelControlFile()
ctl.set_alg_opts(search=search,
alg=alg,
key=3,
epsabs=1e-20,
epsrel=1e-9,
rftol=1e-9,
maxtime=3600,
optional=True,
maximp=maximp,
nnoimp=nnoimp)
ctl.set_data(sfs_data,
n,
dfe=dfe,
c=c,
gamma_r=(-5e4, 1e3),
theta_r=(1e-10, 0.1),
r_r=(0.01, 100),
scale_r=(0.1, 5000.0))
if degree != 50:
ctl.set_dfe_optional_opts(degree=degree, optional=True)
ctl.set_constraint(constraint)
ctl_contents = ctl.construct()
with open(ctl_name, 'w') as control:
control.write(ctl_contents)
res_file_list = out_stem + '.allres.list.txt'
hjids = []
with open(res_file_list, 'w') as res_list:
# split into requested jobs
for i in range(1, spread + 1):
# seed = random.randint(1, 1e6)
seed = i
split_stem = '{}.split{}'.format(out_stem, i)
result_name = split_stem + '.results.txt'
log_name = split_stem + '.log.txt'
print(result_name, file=res_list)
# call anavar
rep_cmd = anavar_cmd.format(path=anavar_path,
ctl=ctl_name,
rslts=result_name,
log=log_name,
seed=seed)
q_sub([rep_cmd],
out=split_stem,
jid=split_stem.split('/')[-1] + '.sh',
t=8,
evolgen=evolgen)
hjids.append(split_stem.split('/')[-1] + '.sh')
# hold job to merge outputs
merge_out = out_stem + '.merged.results.txt'
gather = 'cat {} | gather_searches.py {}'.format(res_file_list, merge_out)
q_sub([gather], out=out_stem + '.merge', hold=hjids, evolgen=evolgen)
def sel_v_neu_anavar(mode, vcf, call, sel_region, constraint, n, c, dfe, alg,
nnoimp, maximp, out_stem, search, degree, spread, evolgen,
start_index, given, ar_ref):
"""
submits anavar jobs to cluster after writing required files etc
:param mode: str
:param vcf: str
:param call: dict
:param sel_region: str
:param constraint: str
:param n: int
:param c: int
:param dfe: str
:param alg: str
:param nnoimp: int
:param maximp: int
:param out_stem: str
:param search: int
:param degree: int
:param spread: int
:param evolgen: bool
:param start_index: int
:param given: bool
:param ar_ref: bool
:return: None
"""
anavar_path = '/shared/evolgen1/shared_data/program_files/sharc/'
anavar_cmd = '{path}anavar1.4 {ctl} {rslts} {log} {seed}'
# sort file names
ctl_name = out_stem + '.control.txt'
merge_out = out_stem + '.merged.results.txt'
# catch given on first run
init = ()
if given:
if not os.path.isfile(merge_out):
sys.exit(
'Given True but no previous runs completed to take besty res from'
)
else:
# get best result from merged out
best_res = an.ResultsFile(
open(merge_out)).ml_estimate(as_string=True)
init = tuple(best_res.split()[3:-1])
# region combinations
region_combs = {
'CDS': ['CDS_frameshift', 'CDS_non_frameshift'],
'intron': ['intron'],
'intergenic': ['intergenic'],
'noncoding': ['intergenic', 'intron']
}
# make control file
if mode == 'snp':
sfs_data = prepare_snp_sfs(vcf,
call,
n,
sel_sfs_regions=region_combs[sel_region],
call_sel_reg=sel_region)
ctl = an.SNPNeuSelControlFile()
else:
sfs_data = prepare_indel_sfs(vcf,
call,
n,
sel_sfs_regions=region_combs[sel_region],
call_sel_reg=sel_region,
ar_ref=ar_ref)
ctl = an.IndelNeuSelControlFile()
ctl.set_alg_opts(search=search,
alg=alg,
key=3,
epsabs=1e-20,
epsrel=1e-9,
rftol=1e-9,
maxtime=3600,
optional=True,
maximp=maximp,
nnoimp=nnoimp,
init=init)
ctl.set_data(sfs_data,
n,
dfe=dfe,
c=c,
gamma_r=(-5e4, 1e5),
theta_r=(1e-14, 0.1),
r_r=(0.01, 100),
scale_r=(0.1, 5000.0))
if degree != 50:
ctl.set_dfe_optional_opts(degree=degree, optional=True)
ctl.set_constraint(constraint)
ctl_contents = ctl.construct()
with open(ctl_name, 'w') as control:
control.write(ctl_contents)
res_file_list = out_stem + '.allres.list.txt'
hjids = []
with open(res_file_list, 'a') as res_list:
# split into requested jobs
for i in range(start_index, start_index + spread):
split_stem = '{}.split{}'.format(out_stem, i)
result_name = split_stem + '.results.txt'
log_name = split_stem + '.log.txt'
print(result_name, file=res_list)
# call anavar
rep_cmd = anavar_cmd.format(path=anavar_path,
ctl=ctl_name,
rslts=result_name,
log=log_name,
seed=i)
q_sub([rep_cmd],
out=split_stem,
jid=split_stem.split('/')[-1] + '.sh',
t=48,
evolgen=evolgen)
hjids.append(split_stem.split('/')[-1] + '.sh')
# hold job to merge outputs
gather = 'cat {} | ~/parus_indel/anavar_analyses/gather_searches.py {}'.format(
res_file_list, merge_out)
q_sub([gather], out=out_stem + '.merge', hold=hjids, evolgen=evolgen)
def sel_v_neu_anavar(sfs_dat, constraint, n, c, dfe, alg, nnoimp, maximp,
out_stem, search, degree, spread, start_index, given):
"""
submits anavar jobs to cluster after writing required files etc
:param sfs_dat: dict
:param constraint: str
:param n: int
:param c: int
:param dfe: str
:param alg: str
:param nnoimp: int
:param maximp: int
:param out_stem: str
:param search: int
:param degree: int
:param spread: int
:param start_index: int
:param given: bool
:return: None
"""
anavar_path = ''
anavar_cmd = '{path}anavar {ctl} {rslts} {log} {seed}'
# sort file names
ctl_name = out_stem + '.control.txt'
merge_out = out_stem + '.merged.results.txt'
# catch given on first run
init = ()
if given:
if not os.path.isfile(merge_out):
sys.exit('Given True but no previous runs completed to take besty res from')
else:
# get best result from merged out
best_res = an.ResultsFile(open(merge_out)).ml_estimate(as_string=True)
init = tuple(best_res.split()[3:-1])
# make control file
ctl = an.SNPNeuSelControlFile()
ctl.set_alg_opts(search=search, alg=alg, key=3,
epsabs=1e-20, epsrel=1e-9, rftol=1e-9,
maxtime=3600, optional=True,
maximp=maximp, nnoimp=nnoimp, init=init)
ctl.set_data(sfs_dat, n, dfe=dfe, c=c, gamma_r=(-500, 100), theta_r=(1e-14, 0.1), r_r=(0.01, 100),
scale_r=(0.1, 5000.0), snp_fold=False)
if degree != 50:
ctl.set_dfe_optional_opts(degree=degree, optional=True)
ctl.set_constraint(constraint)
ctl_contents = ctl.construct()
with open(ctl_name, 'w') as control:
control.write(ctl_contents)
res_file_list = out_stem + '.allres.list.txt'
with open(res_file_list, 'a') as res_list:
# split into requested jobs
for i in range(start_index, start_index+spread):
split_stem = '{}.split{}'.format(out_stem, i)
result_name = split_stem + '.results.txt'
log_name = split_stem + '.log.txt'
print(result_name, file=res_list)
# call anavar
rep_cmd = anavar_cmd.format(path=anavar_path, ctl=ctl_name, rslts=result_name, log=log_name, seed=i)
q_sub([rep_cmd], out=split_stem, jid=split_stem.split('/')[-1] + '.sh', t=48, scheduler='SLURM')