UK Biobank data processing library
Project description
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
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