def get_benchmark_template(config: Dict, software: Software, **kwargs) -> str:
"""
Creates a name template of .tsv output files produced by specific software.
"""
rule_name = kwargs.get("rule_name",
"rule_name keyword argument must be provided")
assert rule_name
template_args = kwargs.copy()
template_args.pop("rule_name")
heuristic = kwargs.get("heuristic", None)
if heuristic:
template_args.pop("heuristic")
# Skip the first character assuming to keep the name convention as
# {pruning}_arg1{arg1}_arg2{arg2}, not p{pruning}_arg1{arg1}...
filename_template = join_kwargs(**template_args)[1:]
software_name = software.name.lower()
if software == PlacementSoftware.EPANG:
valid_heuristics = ("h1", "h2", "h3", "h4")
assert heuristic and heuristic in valid_heuristics, f"{heuristic} is not a valid heuristic."
software_name = software.name.lower() + f"-{heuristic}"
return os.path.join(
cfg.get_work_dir(config), "benchmarks", filename_template + "_" +
software_name + "-" + rule_name + "_benchmark.tsv")
def get_ar_output_templates(config: Dict, arsoft: str) -> List[str]:
"""
Returns a list of resulting files of the ancestral reconstruction stage.
"""
# FIXME: Make a software class for every AR software, and make output directories
# for every AR software
output_dir = os.path.join(cfg.get_work_dir(config), "RAPPAS", "{pruning}",
"red{red}_ar" + arsoft.upper(), "AR")
if arsoft == "PHYML":
output_filenames = [
"extended_align.phylip_phyml_ancestral_seq.txt",
"extended_align.phylip_phyml_ancestral_tree.txt",
"extended_align.phylip_phyml_stats.txt",
"extended_align.phylip_phyml_tree.txt"
]
elif arsoft == "RAXMLNG":
output_filenames = [
"extended_align.phylip.raxml.log",
"extended_align.phylip.raxml.ancestralTree",
"extended_align.phylip.raxml.ancestralProbs",
"extended_align.phylip.raxml.startTree",
"extended_align.phylip.raxml.ancestralStates",
"extended_align.phylip.raxml.rba"
]
elif arsoft == "PAML":
output_filenames = ["rst"]
else:
raise RuntimeError(f"Unknown ancestral reconstruction soft: {arsoft}")
return [
os.path.join(output_dir, filename) for filename in output_filenames
]
def get_experiment_log_dir_template(config: Dict, software: Software) -> str:
"""
Returns a name template of a log directory path for an experiment.
One experiment is conducted by given software with fixed specific
software parameters and a fixed input set (i.e. phylogenetic tree and alignment).
"""
_check_software(software)
software_name = software.value
return os.path.join(cfg.get_work_dir(config), "logs", software_name,
"{pruning}")
def get_software_dir(
config: Dict, software: Union[PlacementSoftware,
AlignmentSoftware]) -> str:
"""
Returns a working directory for given software.
"""
_check_software(software)
work_dir = cfg.get_work_dir(config)
return os.path.join(work_dir, software.value.upper())