Logic for parsing Illumina headers and folders as well as for archiving reads.
git clone https://github.com/PennChopMicrobiomeProgram/seqBackup.git
cd seqBackup/
python -m venv env
source env/bin/activate
pip install -e .
pip install black pytest
Before commits, make sure everything is well formatted and working:
black .
pytest test/
git commit ...
To add a new machine type, add the new machine code to the MACHINE_TYPES map in seqBackuplib/illumina.py. In some cases, you may have to add machine specific parsing in _parse_header or _parse_folder. In test/test_illumina.py, we have a mechanism for requiring tests for each supported machine type. Add the new machine type to the machine_fixtures map and then create the fixture that it points to in test/conftest.py. Follow the pattern laid out by other fixtures and try to make the test data as realistic as possible.
This software is the "source of truth" for Illumina file handling logic. Other software in our ecosystem depend on this logic including the sample registry and the automation pipeline. When you update this software you will have to then update the installed versions wherever it is deployed as a dependency. We don't bother with official GitHub releases and instead just point directly at the master branch, so usually it is a matter of running pip install git+https://github.com/PennChopMicrobiomeProgram/seqBackup.git@master from the host machine.