common.smk

"""Small, shared functions used to generate inputs and parameters.
"""

def _get_beast_analysis(wildcards):
    beast_analysis = _get_beast_analysis_by_build_name(wildcards.build_name)
    return beast_analysis 

def _get_beast_analysis_by_build_name(build_name):
    return [analysis + ".xml" for analysis in config["builds"][build_name].get("beast_analysis")]


def _get_beast_trajectory_analysis(wildcards):
    beast_analysis = _get_beast_trajectory_analysis_by_build_name(wildcards.build_name)
    return beast_analysis 

def _get_beast_trajectory_analysis_by_build_name(build_name):
    return [analysis + ".trajectoryMapper.xml" for analysis in config["builds"][build_name].get("beast_analysis")]


def _get_subsampling_scheme_by_build_name(build_name):
    return config["builds"][build_name].get("subsampling_scheme", build_name)

def _get_metadata_by_build_name(build_name):
    """Returns a path associated with the metadata for the given build name.

    The path can include wildcards that must be provided by the caller through
    the Snakemake `expand` function or through string formatting with `.format`.
    """
    return rules.load.output.metadata
    #if build_name == "global" or "region" not in config["builds"][build_name]:
    #    return rules.load.output.metadata
    #else:
    #    return rules.adjust_metadata_regions.output.metadata

def _get_metadata_by_wildcards(wildcards):
    """Returns a metadata path based on the given wildcards object.

    This function is designed to be used as an input function.
    """
    return _get_metadata_by_build_name(wildcards.build_name)

def _get_sampling_trait_for_wildcards(wildcards):
    if wildcards.build_name in config["exposure"]:
        return config["exposure"][wildcards.build_name]["trait"]
    else:
        return config["exposure"]["default"]["trait"]

def _get_exposure_trait_for_wildcards(wildcards):
    if wildcards.build_name in config["exposure"]:
        return config["exposure"][wildcards.build_name]["exposure"]
    else:
        return config["exposure"]["default"]["exposure"]

def _get_trait_columns_by_wildcards(wildcards):
    if wildcards.build_name in config["traits"]:
        return config["traits"][wildcards.build_name]["columns"]
    else:
        return config["traits"]["default"]["columns"]

def _get_sampling_bias_correction_for_wildcards(wildcards):
    if wildcards.build_name in config["traits"] and 'sampling_bias_correction' in config["traits"][wildcards.build_name]:
        return config["traits"][wildcards.build_name]["sampling_bias_correction"]
    else:
        return config["traits"]["default"]["sampling_bias_correction"]