Importing precalculated data

ELASPIC downloads page

The ELASPIC downloads page contains all precalculated data that is required to run the ELASPIC pipeline on a local machine.

The *.tsv.gz files correspond to different tables of the ELASPIC database:

  • The domain.tar.gz file in the root folder contains Profs domain definitions for files in the PDB, and corresponds to the domain table.
  • The domain_contact.tar.gz file in the root folder contains a list of interactions between those domains, and corresponds to the domain_contact table.
  • All other tables are split into separate folders according to the organism of origin. The files are named using the {table_name}.tsv.gz convention, where table_name is the name of the table in the database.

The *.7z files contain precalculated data:

  • The provean, uniprot_domain, and uniprot_domain_pair subfolders contain precalculated provean supporting sets, and homology models of protein domains and domain-domain interactions, respectively.

Precalculated mutations:

  • The Homo_sapiens folder contains an additional subfolder precalculated_mutations, which contains \(\Delta \Delta G\) scores for mutations in various datasets.

Note

The configure_test.sh and run_test.sh scripts in the ./scripts folder contain examples of how to download and set up a local copy of the database.

Downloading data

In order to run up ELASPIC on a local computer, you need to download precalculated data for your organism of interest. If your goal is to only test the pipeline, you can download a test dataset from the folder current_release/Homo_sapiens_test.

To download all precalculated data for a given organism, use the wget command:

# Download external files
wget -P "${TEST_DIR}/elaspic.kimlab.org" \
    http://elaspic.kimlab.org/static/download/current_release/domain.tsv.gz
wget -P "${TEST_DIR}/elaspic.kimlab.org" \
    http://elaspic.kimlab.org/static/download/current_release/domain_contact.tsv.gz
wget -P "${TEST_DIR}" \
    -r --no-parent --reject "index.html*" --cut-dirs=4  \
    http://elaspic.kimlab.org/static/download/current_release/Homo_sapiens_test/

You need to extract the provean supporting sets and domain homology models into a folder specified by the archive_dir variable in your configuration_file:

mkdir archive  # Set 'archive_dir' variable in the config file to this folder

7z x "${TEST_DIR}/elaspic.kimlab.org/provean/provean.7z" -o"archive"
7z x "${TEST_DIR}/elaspic.kimlab.org/uniprot_domain/uniprot_domain.7z" -o"archive"
7z x "${TEST_DIR}/elaspic.kimlab.org/uniprot_domain_pair/uniprot_domain_pair.7z" -o"archive"

Importing data into a database

You also need to create a local SQL database and fill it with precalculated data.

Modify the database variables in the ELASPIC configuration file to match your local MySQL, PostgreSQL, or SQLite database, and use the elaspic database CLI to create a new database and fill it with precalculated data.

First, you need to create an empty database:

elaspic database -c {your_configuration_file}.ini create

Next, you need to load all precalculated data for the organism in question to your database:

elaspic database -c {your_configuration_file}.ini load_data

To delete the database that you just created, run:

elaspic database -c {your_configuration_file}.ini delete