# -*- coding: utf-8 -*-
"""
Created on Fri Mar 27 12:38:10 2020
@author: jnecus
"""
import os
import pandas as pd
import ukbiobank
[docs]class ukbio:
"""
Parameters
----------
ukb_csv : String, mandatory
Path to ukbiobank csv file. ipthon
Example usage::
import ukbiobank
ukb = ukbiobank.ukbio(ukb_csv='path/to/ukbiobank_data.csv')
Returns
-------
ukbio object.
ukbio objects are required as an input when using ukbiobank-tools functions.
ukbio objects contain import information such as:
- variable codings
- path to ukbiobank csv file
"""
def __init__(self, ukb_csv=None):
file_path = os.path.dirname(__file__)
self.csv_path = ukb_csv
self.data_dict = pd.read_csv(
os.path.join(file_path, "data_coding", "Data_Dictionary_Showcase.csv")
)
# Illness/medication codings
# TODO continue insert coding dictionaries.. (for medications etc..)
self.nonCancerIllnessCoding = pd.read_table(
os.path.join(file_path, "data_coding", "coding6.tsv")
)
self.icd9Coding = pd.read_table(
os.path.join(file_path, "data_coding", "coding87.tsv")
)
self.icd10Coding = pd.read_table(
os.path.join(file_path, "data_coding", "coding19.tsv")
)
# Variable/instance codings
self.field_instance_array_df = ukbiobank.utils.getFieldsInstancesArrays(
ukb_csv=self.csv_path, data_dict=self.data_dict
)