lipidlibrarian 0.4.2

A Lipidomics Database Explorer Package

Lipid Librarian

Build and Installation Instructions

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

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)"