Command Line Interface

After following instructions in the Installation Guide, you should be able to run ELASPIC from the command line using the elaspic command:

$ elaspic --help
usage: elaspic [-h] {run,database,train} ...

optional arguments:
  -h, --help            show this help message and exit

command:
  {run,database,train}
    run                 Run ELASPIC.
    database            Perform maintenance tasks on the ELASPIC database.
    train               Train the ELASPIC classifiers.

Type --help to see the options available for each subcommand:

• elaspic run --help
• elaspic database --help
• elaspic database load_data --help
• etc...

elaspic run

Run the ELASPIC pipeline.

If you wish to mutate an existing PDB, you should specify the name of the PDB file to be mutated, and the mutation(s):

elaspic run \
    --structure_file {structure_file} \
    --mutations {mutations}

If you wish to first create a homology model of a protein, you should provide a fasta file containing the sequence of the protein to be modelled, a PDB file containing the structural template, and the mutation(s):

elaspic run \
    --sequence_file {sequence_file} \
    --structure_file {structure_file} \
    --mutations {mutations}

If you wish to perform mutagenesis on a proteome-wide scale, you need to download protein domain definitions from the elaspic downloads page, and optionally a local copy of the PDB database. After saving your database information to a configuration file, you can run specify the uniprot id and mutation(s):

elaspic run \
  --config_file {config_file} \
  --uniprot_id {uniprot_id} \
  --mutations {mutations}

elaspic train

Train the machine learning predictor for the ELASPIC pipeline.

This is automatically done at install time, and you do not need to do this again unless you update your scikit-learn version.

elaspic database

Perform maintenance tasks on the ELASPIC database.

You must provide a configuration file containing the details of your database installation for any of these commands to work. For more information about configuration files, see Updating the configuration file.

elaspic database create

Create a new database schema.

elaspic database load_data

Load data to the database.

elaspic database delete

Delete the database schema.