The aim of uniprot-redis is to have a rapid access to uniprot data previously stored in redis instance, and querying them by uniprot protein ids.
Start and query uniprot-redis in a python environment with poetry
1. Install and start redis
Install redis following the website instruction : https://redis.io/docs/getting-started/
Then run a redis instance (it needs to run constantly so we recommand to use screen or equivalent)
screen -S redis
redis-server
then ctrl + A + D to quit the screen. screen -r redis if you want to go back to it.
Be aware that it will created a local "save file" of the instance (dump.rdb) in the directory you launch the command. You will need to launch redis-server in the directory where dump.rdb is stored if you want to retrieve the data later.
2. Install uniprot-redis
uniprot-redis is available as a pip package
pip install uniprot-redis
3. Run uniprot-redis and store informations
You need to store into redis the proteins you want to. uniprot-redis can load xml proteome file downloadable here : https://www.uniprot.org/proteomes?query=*
Choose your organisms of interest. For example if you want to have access to all human proteins you will need to download UP000005640 proteome file (https://www.uniprot.org/proteomes/UP000005640) Download => Download all => Format : XML => Download
- Load a proteome into uniprot-redis
- Through python
from uniprot_redis.store import UniprotStore
store = UniprotStore()
protein_collection = store.load_uniprot_xml(file=<xml file>)
# You can identify this protein collection by keyword in order to retrieve it later
store.save_collection('my_id', protein_collection)
# List all collections
store.list_collection()
4. Interrogate uniprot-redis
You can now have an easy access to all stored protein through python code
# Access a protein through its uniprot id
store.get_protein('<uniprot id>')
# Iterator through a collection
store.get_protein_collection('<collection id>')
# Iterator through all proteins stored in the database
store.proteins
5. Uniprot store gestion
# Wipe all database
store.wipe_all()
# Delete a collection
store.delete_collection('<collection id>')
See notebooks/uniprot_redis_demo.ipynb for usage examples
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