def run_simulation(args):
if args.demographic_model is None:
model = stdpopsim.PiecewiseConstantSize(species.population_size)
model.generation_time = species.generation_time
model.citations.extend(species.population_size_citations)
model.citations.extend(species.generation_time_citations)
qc_complete = True
else:
model = get_model_wrapper(species, args.demographic_model)
qc_complete = model.qc_model is not None
if len(args.samples) > model.num_sampling_populations:
exit(
f"Cannot sample from more than {model.num_sampling_populations} "
"populations")
samples = model.get_samples(*args.samples)
contig = species.get_contig(
args.chromosome,
genetic_map=args.genetic_map,
length_multiplier=args.length_multiplier,
length=args.length,
inclusion_mask=args.inclusion_mask,
exclusion_mask=args.exclusion_mask,
)
engine = stdpopsim.get_engine(args.engine)
logger.info(f"Running simulation model {model.id} for {species.id} on "
f"{contig} with {len(samples)} samples using {engine.id}.")
write_simulation_summary(engine=engine,
model=model,
contig=contig,
samples=samples,
seed=args.seed)
if not qc_complete:
warnings.warn(
stdpopsim.QCMissingWarning(
f"{model.id} has not been QCed. Use at your own risk! "
"Demographic models that have not undergone stdpopsim's "
"Quality Control procedure may contain implementation "
"errors, leading to differences between simulations "
"and the model described in the original publication. "
"More information about the QC process can be found in "
"the developer documentation. "
"https://stdpopsim.readthedocs.io/en/latest/development.html"
"#demographic-model-review-process"))
# extract simulate() parameters from CLI args
accepted_params = inspect.signature(engine.simulate).parameters.keys()
kwargs = {k: v for k, v in vars(args).items() if k in accepted_params}
kwargs.update(demographic_model=model, contig=contig, samples=samples)
ts = engine.simulate(**kwargs)
summarise_usage()
if ts is not None:
write_output(ts, args)
# Non-QCed models shouldn't be used in publications, so we skip the
# "If you use this simulation in published work..." citation request.
if qc_complete:
write_citations(engine, model, contig, species)
if args.bibtex_file is not None:
write_bibtex(engine, model, contig, species, args.bibtex_file)
def run_simulation(args):
if args.demographic_model is None:
model = stdpopsim.PiecewiseConstantSize(species.population_size)
model.generation_time = species.generation_time
for citation in species.citations:
reasons = {
stdpopsim.CiteReason.POP_SIZE,
stdpopsim.CiteReason.GEN_TIME,
}
if len(citation.reasons & reasons) > 0:
model.citations.append(citation)
qc_complete = True
else:
model = get_model_wrapper(species, args.demographic_model)
qc_complete = model.qc_model is not None
if len(args.samples) > model.num_sampling_populations:
exit(
f"Cannot sample from more than {model.num_sampling_populations} "
"populations"
)
samples = model.get_samples(*args.samples)
contig = species.get_contig(
args.chromosome,
genetic_map=args.genetic_map,
length_multiplier=args.length_multiplier,
length=args.length,
inclusion_mask=args.inclusion_mask,
exclusion_mask=args.exclusion_mask,
mutation_rate=model.mutation_rate,
)
engine = stdpopsim.get_engine(args.engine)
logger.info(
f"Running simulation model {model.id} for {species.id} on "
f"{contig} with {len(samples)} samples using {engine.id}."
)
# DFE assignment
dfe = None
intervals_summary_str = None
if args.dfe is None:
if args.dfe_interval is not None:
exit(
"A DFE interval has been assigned without a DFE. "
"Please specify a DFE."
)
if args.dfe_annotation is not None:
exit(
"A DFE annotation has been assigned without a DFE. "
"Please specify a DFE."
)
if args.dfe_bed_file is not None:
exit(
"A DFE bed file has been assigned without a DFE. "
"Please specify a DFE."
)
else:
if args.dfe_interval is not None:
if args.dfe_annotation is not None:
exit(
"A DFE annotation and a DFE interval have been "
"selected. Please only use one."
)
if args.dfe_bed_file is not None:
exit(
"A DFE bed file and a DFE interval have been "
"selected. Please only use one."
)
left, right = args.dfe_interval.split(",")
intervals = np.array([[int(left), int(right)]])
intervals_summary_str = f"[{left}, {right})"
if args.dfe_annotation is not None:
if args.dfe_bed_file is not None:
exit(
"A DFE bed file and a DFE annotation have been "
"selected. Please only use one."
)
annot = species.get_annotations(args.dfe_annotation)
intervals = annot.get_chromosome_annotations(args.chromosome)
intervals_summary_str = f"{annot.id} elements on {args.chromosome}"
if args.dfe_bed_file is not None:
intervals = np.loadtxt(args.dfe_bed_file, usecols=[1, 2], dtype="int")
left = np.min(intervals)
right = np.max(intervals)
intervals_summary_str = f"[{left}, {right})"
else:
# case where no intervals specified but we have a DFE
intervals = np.array(
[[0, int(contig.recombination_map.sequence_length)]]
)
intervals_summary_str = f"[{intervals[0][0]}, {intervals[0][1]})"
dfe = species.get_dfe(args.dfe)
contig.add_dfe(
intervals=intervals,
DFE=dfe,
)
logger.info(
f"Applying selection under the DFE model {dfe.id} "
f"in intervals {intervals_summary_str}."
)
write_simulation_summary(
engine=engine,
model=model,
contig=contig,
samples=samples,
dfe=args.dfe,
dfe_interval=intervals_summary_str,
seed=args.seed,
)
if not qc_complete:
warnings.warn(
stdpopsim.QCMissingWarning(
f"{model.id} has not been QCed. Use at your own risk! "
"Demographic models that have not undergone stdpopsim's "
"Quality Control procedure may contain implementation "
"errors, leading to differences between simulations "
"and the model described in the original publication. "
"More information about the QC process can be found in "
"the developer documentation. "
"https://popsim-consortium.github.io/stdpopsim-docs/"
"latest/development.html#demographic-model-review-process"
)
)
# extract simulate() parameters from CLI args
accepted_params = inspect.signature(engine.simulate).parameters.keys()
kwargs = {k: v for k, v in vars(args).items() if k in accepted_params}
kwargs.update(demographic_model=model, contig=contig, samples=samples)
ts = engine.simulate(**kwargs)
summarise_usage()
if ts is not None:
write_output(ts, args)
# Non-QCed models shouldn't be used in publications, so we skip the
# "If you use this simulation in published work..." citation request.
if qc_complete:
write_citations(engine, model, contig, species, dfe)
if args.bibtex_file is not None:
write_bibtex(engine, model, contig, species, args.bibtex_file, dfe)