def refine(tree=None,
aln=None,
ref=None,
dates=None,
branch_length_inference='auto',
confidence=False,
resolve_polytomies=True,
max_iter=2,
precision='auto',
infer_gtr=True,
Tc=0.01,
reroot=None,
use_marginal=False,
fixed_pi=None,
clock_rate=None,
clock_std=None,
clock_filter_iqd=None,
verbosity=1,
covariance=True,
**kwarks):
from treetime import TreeTime
try: #Tc could be a number or 'opt' or 'skyline'. TreeTime expects a float or int if a number.
Tc = float(Tc)
except ValueError:
True #let it remain a string
if (ref is not None) and (fixed_pi is None): #if VCF, fix pi
#Otherwise mutation TO gaps is overestimated b/c of seq length
fixed_pi = [
ref.count(base) / len(ref) for base in ['A', 'C', 'G', 'T', '-']
]
if fixed_pi[-1] == 0:
fixed_pi[-1] = 0.05
fixed_pi = [v - 0.01 for v in fixed_pi]
if ref is not None: # VCF -> adjust branch length
#set branch length mode explicitly if auto, as informative-site only
#trees can have big branch lengths, making this set incorrectly in TreeTime
if branch_length_inference == 'auto':
branch_length_inference = 'joint'
#send ref, if is None, does no harm
tt = TreeTime(tree=tree,
aln=aln,
ref=ref,
dates=dates,
verbose=verbosity,
gtr='JC69',
precision=precision)
# conditionally run clock-filter and remove bad tips
if clock_filter_iqd:
# treetime clock filter will mark, but not remove bad tips
tt.clock_filter(reroot=reroot, n_iqd=clock_filter_iqd,
plot=False) #use whatever was specified
# remove them explicitly
leaves = [x for x in tt.tree.get_terminals()]
for n in leaves:
if n.bad_branch:
tt.tree.prune(n)
print('pruning leaf ', n.name)
# fix treetime set-up for new tree topology
tt.prepare_tree()
if confidence and use_marginal:
# estimate confidence intervals via marginal ML and assign
# marginal ML times to nodes
marginal = 'assign'
else:
marginal = confidence
# uncertainty of the the clock rate is relevant if confidence intervals are estimated
if confidence and clock_std:
vary_rate = clock_std # if standard devivation of clock is specified, use that
elif (clock_rate is None) and confidence and covariance:
vary_rate = True # if run in covariance mode, standard deviation can be estimated
else:
vary_rate = False # otherwise, rate uncertainty will be ignored
tt.run(infer_gtr=infer_gtr,
root=reroot,
Tc=Tc,
time_marginal=marginal,
branch_length_mode=branch_length_inference,
resolve_polytomies=resolve_polytomies,
max_iter=max_iter,
fixed_pi=fixed_pi,
fixed_clock_rate=clock_rate,
vary_rate=vary_rate,
use_covariation=covariance,
**kwarks)
if confidence:
for n in tt.tree.find_clades():
n.num_date_confidence = list(tt.get_max_posterior_region(n, 0.9))
print(
"\nInferred a time resolved phylogeny using TreeTime:"
"\n\tSagulenko et al. TreeTime: Maximum-likelihood phylodynamic analysis"
"\n\tVirus Evolution, vol 4, https://academic.oup.com/ve/article/4/1/vex042/4794731\n"
)
return tt
def refine(tree=None, aln=None, ref=None, dates=None, branch_length_inference='auto',
confidence=False, resolve_polytomies=True, max_iter=2,
infer_gtr=True, Tc=0.01, reroot=None, use_marginal=False, fixed_pi=None,
clock_rate=None, clock_std=None, clock_filter_iqd=None, verbosity=1, **kwarks):
from treetime import TreeTime
try: #Tc could be a number or 'opt' or 'skyline'. TreeTime expects a float or int if a number.
Tc = float(Tc)
except ValueError:
True #let it remain a string
if (ref is not None) and (fixed_pi is None): #if VCF, fix pi
#Otherwise mutation TO gaps is overestimated b/c of seq length
fixed_pi = [ref.count(base)/len(ref) for base in ['A','C','G','T','-']]
if fixed_pi[-1] == 0:
fixed_pi[-1] = 0.05
fixed_pi = [v-0.01 for v in fixed_pi]
if ref is not None: # VCF -> adjust branch length
#set branch length mode explicitly if auto, as informative-site only
#trees can have big branch lengths, making this set incorrectly in TreeTime
if branch_length_inference == 'auto':
branch_length_inference = 'joint'
#send ref, if is None, does no harm
tt = TreeTime(tree=tree, aln=aln, ref=ref, dates=dates,
verbose=verbosity, gtr='JC69')
# conditionally run clock-filter and remove bad tips
if clock_filter_iqd:
# treetime clock filter will mark, but not remove bad tips
tt.clock_filter(reroot='best', n_iqd=clock_filter_iqd, plot=False)
# remove them explicitly
leaves = [x for x in tt.tree.get_terminals()]
for n in leaves:
if n.bad_branch:
tt.tree.prune(n)
print('pruning leaf ', n.name)
# fix treetime set-up for new tree topology
tt.prepare_tree()
if confidence and use_marginal:
# estimate confidence intervals via marginal ML and assign
# marginal ML times to nodes
marginal = 'assign'
else:
marginal = confidence
vary_rate = False
if clock_rate and clock_std:
vary_rate = clock_std
else:
vary_rate = True
tt.run(infer_gtr=infer_gtr, root=reroot, Tc=Tc, time_marginal=marginal,
branch_length_mode=branch_length_inference, resolve_polytomies=resolve_polytomies,
max_iter=max_iter, fixed_pi=fixed_pi, fixed_clock_rate=clock_rate,
vary_rate=vary_rate, **kwarks)
if confidence:
for n in tt.tree.find_clades():
n.num_date_confidence = list(tt.get_max_posterior_region(n, 0.9))
print("\nInferred a time resolved phylogeny using TreeTime:"
"\n\tSagulenko et al. TreeTime: Maximum-likelihood phylodynamic analysis"
"\n\tVirus Evolution, vol 4, https://academic.oup.com/ve/article/4/1/vex042/4794731\n")
return tt
def estimate_clock_model(params):
"""
implementing treetime clock
"""
if assure_tree(params, tmp_dir='clock_model_tmp'):
return 1
dates = utils.parse_dates(params.dates, date_col=params.date_column, name_col=params.name_column)
if len(dates)==0:
return 1
outdir = get_outdir(params, '_clock')
###########################################################################
### READ IN VCF
###########################################################################
#sets ref and fixed_pi to None if not VCF
aln, ref, fixed_pi = read_if_vcf(params)
is_vcf = True if ref is not None else False
###########################################################################
### ESTIMATE ROOT (if requested) AND DETERMINE TEMPORAL SIGNAL
###########################################################################
if params.aln is None and params.sequence_length is None:
print("one of arguments '--aln' and '--sequence-length' is required.", file=sys.stderr)
return 1
basename = get_basename(params, outdir)
try:
myTree = TreeTime(dates=dates, tree=params.tree, aln=aln, gtr='JC69',
verbose=params.verbose, seq_len=params.sequence_length,
ref=ref)
except TreeTimeError as e:
print("\nTreeTime setup failed. Please see above for error messages and/or rerun with --verbose 4\n")
raise e
myTree.tip_slack=params.tip_slack
if params.clock_filter:
n_bad = [n.name for n in myTree.tree.get_terminals() if n.bad_branch]
myTree.clock_filter(n_iqd=params.clock_filter, reroot=params.reroot or 'least-squares')
n_bad_after = [n.name for n in myTree.tree.get_terminals() if n.bad_branch]
if len(n_bad_after)>len(n_bad):
print("The following leaves don't follow a loose clock and "
"will be ignored in rate estimation:\n\t"
+"\n\t".join(set(n_bad_after).difference(n_bad)))
if not params.keep_root:
# reroot to optimal root, this assigns clock_model to myTree
if params.covariation: # this requires branch length estimates
myTree.run(root="least-squares", max_iter=0,
use_covariation=params.covariation)
try:
res = myTree.reroot(params.reroot,
force_positive=not params.allow_negative_rate)
except TreeTimeError as e:
print("ERROR: unknown root or rooting mechanism!")
raise e
myTree.get_clock_model(covariation=params.covariation)
else:
myTree.get_clock_model(covariation=params.covariation)
d2d = utils.DateConversion.from_regression(myTree.clock_model)
print('\n',d2d)
print(fill('The R^2 value indicates the fraction of variation in'
'root-to-tip distance explained by the sampling times.'
'Higher values corresponds more clock-like behavior (max 1.0).')+'\n')
print(fill('The rate is the slope of the best fit of the date to'
'the root-to-tip distance and provides an estimate of'
'the substitution rate. The rate needs to be positive!'
'Negative rates suggest an inappropriate root.')+'\n')
print('\nThe estimated rate and tree correspond to a root date:')
if params.covariation:
reg = myTree.clock_model
dp = np.array([reg['intercept']/reg['slope']**2,-1./reg['slope']])
droot = np.sqrt(reg['cov'][:2,:2].dot(dp).dot(dp))
print('\n--- root-date:\t %3.2f +/- %1.2f (one std-dev)\n\n'%(-d2d.intercept/d2d.clock_rate, droot))
else:
print('\n--- root-date:\t %3.2f\n\n'%(-d2d.intercept/d2d.clock_rate))
if not params.keep_root:
# write rerooted tree to file
outtree_name = basename+'rerooted.newick'
Phylo.write(myTree.tree, outtree_name, 'newick')
print("--- re-rooted tree written to \n\t%s\n"%outtree_name)
table_fname = basename+'rtt.csv'
with open(table_fname, 'w') as ofile:
ofile.write("#name, date, root-to-tip distance\n")
ofile.write("#Dates of nodes that didn't have a specified date are inferred from the root-to-tip regression.\n")
for n in myTree.tree.get_terminals():
if hasattr(n, "raw_date_constraint") and (n.raw_date_constraint is not None):
if np.isscalar(n.raw_date_constraint):
tmp_str = str(n.raw_date_constraint)
elif len(n.raw_date_constraint):
tmp_str = str(n.raw_date_constraint[0])+'-'+str(n.raw_date_constraint[1])
else:
tmp_str = ''
ofile.write("%s, %s, %f\n"%(n.name, tmp_str, n.dist2root))
else:
ofile.write("%s, %f, %f\n"%(n.name, d2d.numdate_from_dist2root(n.dist2root), n.dist2root))
for n in myTree.tree.get_nonterminals(order='preorder'):
ofile.write("%s, %f, %f\n"%(n.name, d2d.numdate_from_dist2root(n.dist2root), n.dist2root))
print("--- wrote dates and root-to-tip distances to \n\t%s\n"%table_fname)
###########################################################################
### PLOT AND SAVE RESULT
###########################################################################
plot_rtt(myTree, outdir+params.plot_rtt)
return 0
def estimate_clock_model(params):
"""
implementing treetime clock
"""
if assure_tree(params, tmp_dir='clock_model_tmp'):
return 1
dates = utils.parse_dates(params.dates)
if len(dates)==0:
return 1
outdir = get_outdir(params, '_clock')
###########################################################################
### READ IN VCF
###########################################################################
#sets ref and fixed_pi to None if not VCF
aln, ref, fixed_pi = read_if_vcf(params)
is_vcf = True if ref is not None else False
###########################################################################
### ESTIMATE ROOT (if requested) AND DETERMINE TEMPORAL SIGNAL
###########################################################################
if params.aln is None and params.sequence_length is None:
print("one of arguments '--aln' and '--sequence-length' is required.", file=sys.stderr)
return 1
basename = get_basename(params, outdir)
myTree = TreeTime(dates=dates, tree=params.tree, aln=aln, gtr='JC69',
verbose=params.verbose, seq_len=params.sequence_length,
ref=ref)
myTree.tip_slack=params.tip_slack
if myTree.tree is None:
print("ERROR: tree loading failed. exiting...")
return 1
if params.clock_filter:
n_bad = [n.name for n in myTree.tree.get_terminals() if n.bad_branch]
myTree.clock_filter(n_iqd=params.clock_filter, reroot=params.reroot or 'least-squares')
n_bad_after = [n.name for n in myTree.tree.get_terminals() if n.bad_branch]
if len(n_bad_after)>len(n_bad):
print("The following leaves don't follow a loose clock and "
"will be ignored in rate estimation:\n\t"
+"\n\t".join(set(n_bad_after).difference(n_bad)))
if not params.keep_root:
# reroot to optimal root, this assigns clock_model to myTree
if params.covariation: # this requires branch length estimates
myTree.run(root="least-squares", max_iter=0,
use_covariation=params.covariation)
res = myTree.reroot(params.reroot,
force_positive=not params.allow_negative_rate)
myTree.get_clock_model(covariation=params.covariation)
if res==ttconf.ERROR:
print("ERROR: unknown root or rooting mechanism!\n"
"\tvalid choices are 'least-squares', 'ML', and 'ML-rough'")
return 1
else:
myTree.get_clock_model(covariation=params.covariation)
d2d = utils.DateConversion.from_regression(myTree.clock_model)
print('\n',d2d)
print('The R^2 value indicates the fraction of variation in'
'\nroot-to-tip distance explained by the sampling times.'
'\nHigher values corresponds more clock-like behavior (max 1.0).')
print('\nThe rate is the slope of the best fit of the date to'
'\nthe root-to-tip distance and provides an estimate of'
'\nthe substitution rate. The rate needs to be positive!'
'\nNegative rates suggest an inappropriate root.\n')
print('\nThe estimated rate and tree correspond to a root date:')
if params.covariation:
reg = myTree.clock_model
dp = np.array([reg['intercept']/reg['slope']**2,-1./reg['slope']])
droot = np.sqrt(reg['cov'][:2,:2].dot(dp).dot(dp))
print('\n--- root-date:\t %3.2f +/- %1.2f (one std-dev)\n\n'%(-d2d.intercept/d2d.clock_rate, droot))
else:
print('\n--- root-date:\t %3.2f\n\n'%(-d2d.intercept/d2d.clock_rate))
if not params.keep_root:
# write rerooted tree to file
outtree_name = basename+'rerooted.newick'
Phylo.write(myTree.tree, outtree_name, 'newick')
print("--- re-rooted tree written to \n\t%s\n"%outtree_name)
table_fname = basename+'rtt.csv'
with open(table_fname, 'w') as ofile:
ofile.write("#name, date, root-to-tip distance\n")
ofile.write("#Dates of nodes that didn't have a specified date are inferred from the root-to-tip regression.\n")
for n in myTree.tree.get_terminals():
if hasattr(n, "raw_date_constraint") and (n.raw_date_constraint is not None):
if np.isscalar(n.raw_date_constraint):
tmp_str = str(n.raw_date_constraint)
elif len(n.raw_date_constraint):
tmp_str = str(n.raw_date_constraint[0])+'-'+str(n.raw_date_constraint[1])
else:
tmp_str = ''
ofile.write("%s, %s, %f\n"%(n.name, tmp_str, n.dist2root))
else:
ofile.write("%s, %f, %f\n"%(n.name, d2d.numdate_from_dist2root(n.dist2root), n.dist2root))
for n in myTree.tree.get_nonterminals(order='preorder'):
ofile.write("%s, %f, %f\n"%(n.name, d2d.numdate_from_dist2root(n.dist2root), n.dist2root))
print("--- wrote dates and root-to-tip distances to \n\t%s\n"%table_fname)
###########################################################################
### PLOT AND SAVE RESULT
###########################################################################
plot_rtt(myTree, outdir+params.plot_rtt)
return 0