README.md

cycIF-DB

This library provides simple APIs to manage cycIF quantification data.

Install this library in place

pip install -e .

Install postgresql and configure privileges in cloud server(s)

ansible-playbook -i playbook/inventory.yml playbook/install_db.yml

Install dependencies

pip install -r requirements.txt

Deploy database from scratch

python scripts/create_db.py

Upgrade database

alembic upgrade head

Downgrade database

alembic downgrade -1

Autogenerate a revision

alembic revision --autogenerate -m "{slug}" --rev-id {id}

Download quantification datasets from Galaxy

python scripts/download_datasets.py {sample_name} {datasets_id} [{datasets_id} ...]

Load or update markers and their aliases

python scripts/insert_or_sync_stock_markers.py

Add a sample compex into database

python scripts/add_sample_complex.py -d {folder / sample_name}

or

python scripts/add_sample_complex.py "{sample_name}__{tag}" {path_to_cells} {path_to_markers}

Python APIs

Construct session object

from cycif_db import CycSession

csess = CycSession()

List samples

sample_list = csess.list_samples(detailed=False)

Output a pandas DataFrame for all quantification features associated a sample

df = csess.get_cells_for_sample(sample/sample_id, to_path=None)

Output a pandas DataFrame for all common features associated with multiple samples

df = csess.get_cells_from_samples(sample_list/sample_id_list, marker_filter='intersection', to_path=None)

Close session object

csess.close()