ukbparse 0.10.1

UK Biobank data processing library

ukbparse is a Python library for pre-processing of UK BioBank data.

Installation

Install ukbparse via pip:

pip install ukbparse

Usage

Comprehensive documentation has not yet been written.

General usage is as follows:

ukbparse [options] output.tsv input1.tsv input2.tsv

You can get information on all of the options by typing ukbparse --help.

Options can be specified on the command line, and/or stored in a configuration file. For example, the options in the following command line:

ukbparse \
  --overwrite \
  --import_all \
  --log_file log.txt \
  --icd10_map_file icd_codes.tsv \
  --category 10 \
  --category 11 \
  output.tsv input1.tsv input2.tsv

Could be stored in a configuration file config.txt:

overwrite
import_all
log_file       log.txt
icd10_map_file icd_codes.tsv
category       10
category       11

And then executed as follows:

ukbparse -cfg config.txt output.tsv input1.tsv input2.tsv

Tests

To run the test suite, you need to install some additional dependencies:

pip install -r requirements-dev.txt

Then you can run the test suite using pytest:

pytest