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