lipidlibrarian 0.5.1

A Lipidomics Database Explorer Package

Lipid Librarian

Build and Installation Instructions

Make sure you've installed python 3.11 and are using this version to create the virtual environment as well. If you experience slow performance, consider running a local SQL server to serve the ALEX¹²³ database instead of reading it from a file, or disable ALEX¹²³ for your queries.

Python Virtual Environment

make install install_optional

Docker Container

docker build -t lipidlibrarian -f Containerfile .

OCI Container for Docker/Podman/Kubernetes

buildah build -t lipidlibrarian -f Containerfile .

Test Lipid Librarian

Run pytest in the git root directory with a venv activated with LipidLibrarian installed. It is highly recommended to run a local ALEX123 SQL Database for performance reasons (see below)

pytest

Run Lipid Librarian

CLI

In case you installed Lipid Librarian into a 'venv' virtual environment, make sure you activate it before with source venv/bin/activate.

lipidlibrarian "PC(18:1_20:0)" "PE 38:1" "816.6477;0.001;+H+" "Cholesterol" "SLM:000487065"
lipidlibrarian path/to/file
cat path/to/file | lipidlibrarian

Docker

docker run lipidlibrarian "PC(18:1_20:0)" "PE 38:1" "816.6477;0.001;+H+" "Cholesterol" "SLM:000487065"

Podman

podman run lipidlibrarian "PC(18:1_20:0)" "PE 38:1" "816.6477;0.001;+H+" "Cholesterol" "SLM:000487065"

Import Python Package

from lipidlibrarian.LipidQuery import *

query1 = LipidQuery("PC(18:1_20:0)").query()
query2 = LipidQuery("PE 38:1").query()
query3 = LipidQuery("816.6477;0.001;+H+").query()
query4 = LipidQuery("Cholesterol").query()
query5 = LipidQuery("SLM:000487065").query()

for lipid in query1:
    print(repr(lipid))

for lipid in query2:
    print(format(lipid, 'json'))

for lipid in query3:
    print(format(lipid, 'html'))

for lipid in query4:
    print(repr(lipid))

for lipid in query5:
    print(repr(lipid))

Run a local ALEX¹²³ SQL Database

The performance of querying the ALEX¹²³ database is quite low, as the whole file has to be parsed into memory first. To alleviate this issue, run a local SQL database to serve the information from ALEX¹²³ to lipidlibrarian:

from an SQL dump file:

mkdir -p data/alex123/sql
gdown 1K5-PnK9HEA5L0Y79CaLgFMKOQGddDSgi -O data/alex123/sql/alex123_db.sql

podman  run --detach --name alex123-sql --env MARIADB_ALLOW_EMPTY_ROOT_PASSWORD=1 --env MARIADB_USER=alex123 --env MARIADB_PASSWORD=alex123 --env MARIADB_DATABASE=alex123 -p 3306:3306 -v ./data/alex123/sql:/docker-entrypoint-initdb.d:O  mariadb:latest

or alternatively:

podman run --detach --name alex123-sql --env MARIADB_ALLOW_EMPTY_ROOT_PASSWORD=1 --env MARIADB_USER=alex123 --env MARIADB_PASSWORD=alex123 --env MARIADB_DATABASE=alex123 -p 3306:3306  docker.io/library/mariadb:latest

sync_alex123_sql_database --sql mysql+pymysql://alex123:alex123@127.0.0.1:3306/alex123

lipidlibrarian --sql --sql-host 127.0.0.1 --sql-port 3306 --sql-user alex123 --sql-password alex123 --sql-database alex123 "PC(18:1_20:0)"

from this container you can create the SQL dump file:

podman exec alex123-sql mariadb-dump --user alex123 --password=alex123 alex123 > alex123_db.sql