def get_common_template_args(config: Dict) -> Dict[str, Any]:
"""
Each placement query has a template name based on two type of inputs:
1) common arguments: tree and query sequences -- independent of software
2) specific arguments: model params etc. -- depends on software used
This method creates a dict of common template arguments that can be passed to
'expand' function of snakemake to resolve the common query name template given
by get_common_queryname_template().
"""
if cfg.get_mode(config) == cfg.Mode.LIKELIHOOD:
return {
"pruning": ["0"],
"length": ["0"],
"query": fasta.get_sequence_ids(config["query_user"])
}
else:
return {
"pruning": range(config["pruning_count"]),
"length": config["read_length"]
}
def get_name_prefix(config: Dict) -> str:
return "query" if cfg.get_mode(
config) == cfg.Mode.LIKELIHOOD else "pruning"