def __init__(self):
self.logger = Logger()
self.sample_s = None
self.geno_df = None
self.group_col = None
self.agg_col = None
self.agg_cat_l = None
def __init__(self, cohort_fam):
self.logger = Logger()
self.node_generator = NodeGenerator()
cohort_df = pd.read_csv(cohort_fam, sep="\t", dtype=str)
self.logger.log("Making family tree objects...")
self.fam_tree_l = cohort_df.groupby("FAMILY").apply(
self.make_fam_tree).tolist()
self.fam_tree_l = natsorted(self.fam_tree_l,
key=lambda fam_tree: fam_tree.id)
def __init__(self,bf_file=None,wf_file=None,cohort_fam=None,kinship_coef_thresh_dict={"0":0.354,"1":0.177,"2":0.0844,"3":0.0442}):
self.logger = Logger()
self.bf_file = bf_file
self.wf_file = wf_file
self.kinship_coef_thresh_dict = kinship_coef_thresh_dict
self.cohort_fam = cohort_fam
self.bf_df = None
self.wf_df = None
self.cohort_df = None
def __init__(self,
name,
category,
A_l,
N_l,
A_n_min=0,
N_n_min=0,
A_p_min=None,
AN_p_diff_min=None):
self.logger = Logger()
self.name = name
self.category = category
self.A_l = natsorted(A_l)
self.N_l = natsorted(N_l)
self.A_n_min = A_n_min
self.N_n_min = N_n_min
self.A_p_min = A_p_min
self.AN_p_diff_min = AN_p_diff_min
def __init__(self, scripts_dir): self.logger = Logger() self.scripts_dir = scripts_dir