Running the tests

Warning

The tests are currently broken in multiple ways (internal errors plus irrelevant tests) therefore they should not be used to test your POSTGAP installation.

This is the testing README

Testing POSTGAP output

The tests folder contains three types of quality control utilities for POSTGAP output, namely health checks, data checks and reports.

Health checks

These are unit tests that:

• check the data schema, such as:
  • consistent format for all values in a column
  • uniqueness of values in a column, when grouped by values in another
• can be run against either a partial or whole output file, such as:
  • an output file for a single EFO term
  • a large concatenated output file (across all EFO terms)

Data checks

These are unit tests that:

• check biological expectations, such as:
  • filtering of the MHC region
  • filtering of trans relations (ie. when genes and snps have different chromosomes)
• can be run against a whole output file only

Reports

These are summary or metadata files that:

• can be generated for either a partial or whole output file present summary statistics to allow comparison between POSTGAP output files

Usage

Installation requirements

Assumption: You have python3 installed.

Ideally, use virtualenv as follows:

# (in tests folder)
virtualenv -p python3 venv
source venv/bin/activate
pip install -r requirements.txt

Run tests against a file

For a file in POSTGAP TSV format, run:

python runner.py ./sample_data/postgap.20180108.asthma.tsv.gz

Run report generator against a file

For a file in POSTGAP TSV format, run:

python reporter.py ./sample_data/postgap.20180108.asthma.tsv.gz

This will produce a file in tests/__reports__ with filename format format <input_file>.REPORT.<timestamp>.ipynb.