def __init__(self, args):
"""
These arguments are specifically to assist with PGS SummaryCLeaner
"""
super().__init__(args)
self._config = self.config["Summary"]
# Set the write directory for Summary Files
self.make_sub_directory("PGS", "Cleaned")
self.summary_directory = Path(self.working_dir, "PGS", "Cleaned")
# Validate the summary file, and set the load type, sample size and header indexing
self.summary_file = mc.validate_path(self.args["Summary_Path"])
self.zipped, self.sample_size = self._set_summary_stats()
self._summary_headers = self._set_summary_headers()
# Determine effect type, and load the configuration of alleles, set z scores if requried
self.effect_type = self._set_effect_type(
self.args["Summary_Effect_Type"])
self.ambiguous_snps, self.allowed_alleles, self.allele_flip = self._configure_alleles(
)
self.z_scores = self._set_z_scores(self.args["Z_Scores"])
self.summary_headers, self.summary_dict = self._set_summary_write_headers(
)
def __init__(self, args):
"""
These attributes are or can be used by multiple processors so are not restricted to sub-loaders
:param args:
"""
super().__init__(args)
self.target_chromosome = self.args["Target_Chromosome"]
# Internal data brought across with package, loaded if requested
self.hap_map_3 = self._load_local_data_path("HapMap3")
self.lr_ld_path = self._load_local_data_path("Filter_Long_Range_LD")
# Genetic files attributes
self.gen_directory = validate_path(self.args["Load_Directory"])
self.gen_type = self.args["Load_Type"]
self._snp_tools = self.args["PySnpTools_Bgen"]
# PySnpTools will by default write memory files to the directory of the Gen files, but this is often undesirable
# on a sever environment where read and write permissions may not be universal.
if self._snp_tools:
self.make_sub_directory(None, "PySnpTools_Meta")
custom_meta_path(Path(self.working_dir, "PySnpTools_Meta"))
# A list of iid to be used for a reference panel if required
self.ref_panel = self._set_reference_panel()
def _set_reference_panel(self):
"""
Many operations will need a reference panel of individuals that are genetically dis-similar/ Not related to each
other. This will load a csv or similar text file with two columns of type FID - IID if set. Else will return
None.
Note
-----
This operation does NOT allow for headers, so do not set them!
"""
if self.args["Reference_Panel"]:
path_to_file = Path(self.args["Reference_Panel"])
validate_path(path_to_file, False)
return CsvObject(path_to_file, set_columns=True, file_headers=False).row_data
else:
return None
def __init__(self, args):
"""
Loads args into memory to be used by other Loaders to initialise Input
Contains common names as attributes so that they can be used as arguments to avoid spelling/alternative naming
where-ever possible
"""
self.args = set_args(args)
self.working_dir = validate_path(self.args["Working_Directory"], False)
self.config = load_yaml(Path(Path(__file__).parent, "Config.yaml"))
def __init__(self, args):
"""
This Class Loads all other Loaders that represent specific or common attributes/methods that are used across
processors.
Methods or attributes set within this class are dependent on multiple attributes from its inherited sub class or
are specific to Input
:param args: Args Passed by the users
"""
super().__init__(args)
# General operational parameters
self.operation = set_current_job(self.args["Operation"])
self.iter_size = self.args["Iter_Size"]
# Score information
self.make_sub_directory("PGS", "Scores")
self.scores_directory = Path(self.working_dir, "PGS", "Scores")
# todo expose this but have a default
self.score_type = "Inf_Weights"
self.phenotype_file = validate_path(self.args["Phenotype"])
self.covariates_file = validate_path(self.args["Covariates"])