CLI Docs¶

marsi provides a command line interface (CLI) that allows running marsi from the command line.

The CLI is split in three parts.

marsi db

marsi optimize

marsi chem

marsi db¶

Contains the commands to build the chemical analogues database.

To get started type:

$ marsi db init

This will take a few hours to download the necessary files.

The commands under this subcommand are used to perform constraint-based modeling.

There are two main functions:

$ marsi optimize mutagenesis

will calculate knockout-based designs. And

$ marsi optimize ale

will calculate knockout based and over-, down-regulated designs.

The chem subcommand can be used to search the chemical analogues database.

$ marsi chem find-analogs --inchi=<inchi-str>