def run_mcmc3r(indir, odir, intree, clock=2, usedata=1):
if not exists(odir):
os.system(f'mkdir -p {odir}')
ctl = glob(f"{indir}/*.ctl")
if not ctl:
raise IOError('not ctl file')
os.system(f'cp {ctl[0]} {odir}/04_mcmctree.ctl')
os.system(f'ln -sf `realpath {indir}/in.BV` {odir}/')
param = {
'treefile': intree,
'clock': clock,
'usedata': '1' if usedata == 1 else '2 ../in.BV 1',
# 'seqtype': '0'
}
text = modify(f'{odir}/04_mcmctree.ctl', **param)
with open(f'{odir}/04_mcmctree.ctl', 'w') as f1:
f1.write(text)
cmd = f"""/home-user/thliao/anaconda3/envs/r_env/bin/R -e "setwd('{odir}'); b = mcmc3r::make.beta(n=8, a=5, method='step-stones'); mcmc3r::make.bfctlf(b, ctlf='04_mcmctree.ctl', betaf='beta.txt')" """
check_call(cmd, shell=1, executable='/home-user/thliao/anaconda3/bin/zsh')
_ctl = "04_mcmctree.ctl"
cmds = []
for _ in range(1, 9):
cmds.append(f"cd {odir}/{_}/ ; mcmctree {_ctl} > run.log ")
return cmds
def run_mcmc3r(indir, odir, intree, clock=2, usedata=1):
if not exists(odir):
os.system(f'mkdir -p {odir}')
os.system(f'cp {indir}/04_mcmctree.ctl {odir}/')
os.system(f'ln -s `realpath {indir}/in.BV` {odir}/')
param = {
'treefile': intree,
'clock': clock,
'usedata': '1' if usedata == 1 else '2 ../in.BV 1',
# 'seqtype': '0'
}
text = modify(f'{odir}/04_mcmctree.ctl', **param)
with open(f'{odir}/04_mcmctree.ctl', 'w') as f1:
f1.write(text)
cmd = f""" `which R` -e "setwd('{odir}'); b = mcmc3r::make.beta(n=8, a=5, method='step-stones'); mcmc3r::make.bfctlf(b, ctlf='04_mcmctree.ctl', betaf='beta.txt')" """
check_call(cmd, shell=1, executable='/home-user/thliao/anaconda3/bin/zsh')
target_ = ['set33', 'set34', 'set35', 'set36', 'set37']
target_dir = './AR_set1'
for t in target_:
for model in ['IR', 'AR']:
if not exists(f"./{model}_{t}"):
os.makedirs(f"./{model}_{t}")
os.system(f'cp {target_dir}/03_mcmctree.ctl ./{model}_{t}/')
param = {
'treefile':
"/share/home-user/thliao/data/plancto/dating_for/cal_tree/83g_set1.newick"
.replace('set1', t),
'clock':
2 if model == 'IR' else 3
}
text = modify(f'./{model}_{t}/03_mcmctree.ctl', **param)
with open(f'./{model}_{t}/03_mcmctree.ctl', 'w') as f1:
f1.write(text)
cmd = f"""R -e "setwd('{model}_{t}'); b = mcmc3r::make.beta(n=8, a=5, method='step-stones'); mcmc3r::make.bfctlf(b, ctlf='03_mcmctree.ctl', betaf='beta.txt')" """
os.system(cmd)
cmd = f"""R -e "setwd('IR_{t}'); b = mcmc3r::make.beta(n=8, a=5, method='step-stones'); mcmc3r::make.bfctlf(b, ctlf='03_mcmctree.ctl', betaf='beta.txt')" """
os.system(cmd)
_ctl = "03_mcmctree.ctl"
cmds = []
for t in target_:
for _ in range(1, 9):
for model in ['IR', 'AR']:
cmds.append(
f"cd {model}_{t}/{_}/ ; mcmctree {_ctl} > run.log ")
def generate_batch_mcmc(cal_trees,
template_dir,
odir,
program_name='',
clock_t='2',
seqtype='nucl',
seqfile=None,
print=1,
sampfreq=20,
nsample=20000,
burnin=2000):
"""generate batch mcmc directory according to the template dir which contains the precalculated in.BV file.
Args:
cal_trees (dict): dict of calibrated trees with the set name as their key.
template_dir (str): dir with in.BV
odir (str): ouput directroy, it will automated generate descending directory following f"{odir}/{program_name}/{seqtype}/clock{clock_t}".
program_name (str, optional): for generated ouput directory. Defaults to ''.
clock_t (str, optional): 3 for AR. 2 for IR . Defaults to '2'.
seqtype (str, optional): [description]. Defaults to 'nucl'.
seqfile (str, optional): [description]. Defaults to None.
print (int, optional): [description]. Defaults to 1.
sampfreq (int, optional): [description]. Defaults to 20.
nsample (int, optional): [description]. Defaults to 20000.
burnin (int, optional): [description]. Defaults to 2000.
Returns:
list: list of commands suitable to run mcmc
"""
odir = f"{odir}/{program_name}/{seqtype}/clock{clock_t}"
cmds = []
for cal_name, cal_tree in cal_trees.items():
set_name = cal_name
pre_ctl = glob(f'{template_dir}/*.ctl')
if not pre_ctl:
continue
else:
pre_ctl = pre_ctl[0]
inbv = abspath(glob(f'{template_dir}/in.BV')[0])
param = {
# 'seqfile': seqfile_b,
'treefile': abspath(cal_tree),
# 'ndata': ndata,
# 'seqtype': seqtype,
'usedata': "2 in.BV 1",
'outfile': './03_mcmctree.out',
'clock': clock_t,
# 'BDparas': bd_paras,
'rgene_gamma': '1 100 1' if seqtype == 'nucl' else '1 30 1',
# 'sigma2_gamma': sigma2_gamma,
'burnin': burnin,
'sampfreq': sampfreq,
'nsample': nsample,
# 'alpha': 0.5,
'print': print
}
if seqfile is not None:
param['seqfile'] = seqfile
# modify these ctl
for repeat_n in ['run1', 'run2']:
onew_name = f'{set_name}_{repeat_n}'
if exists(pre_ctl):
# prepare dir and soft link the in.BV
final_odir = join(odir, onew_name)
os.makedirs(final_odir, exist_ok=True)
os.system(f"ln -sf {inbv} {final_odir}/ ")
output_ctl = join(final_odir, '04_mcmctree.ctl')
# generate the text
text = modify(pre_ctl, **param)
with open(output_ctl, 'w') as f1:
f1.write(text)
# generate the command
cmd = f"cd {join(final_odir)} ; mcmctree ./04_mcmctree.ctl > ./run.log "
# check the completeness of previous run
if not exists(join(final_odir, 'FigTree.tre')):
cmds.append(cmd)
if exists(join(final_odir, 'mcmc.txt')):
# if not figTree.tre but mcmc.txt, it means it doesn't complete at last time
os.system(f"rm {join(final_odir, 'mcmc.txt')} ")
return cmds