AbExp web interface

This is the web interface for the AbExp project, based on the AbSplice-web-interface. It is a simple web interface that allows users to get the AbExp scores for precomputed variants. The web interface is built using the Flask web framework.

Dataset

The app requires the following files to run. Test files can be found in the example_files directory.

• A parquet file containing the precomputed AbExp scores for various genome-gene-variant-tissue combinations. The file may be partitioned.
  • File name: abexp.parquet:
  • Columns:
    • genome
    • chrom
    • start # (0-based)
    • end # (1-based)
    • ref
    • alt
    • gene
    • tissue
    • tissue_type
    • <score_column> # The default is abexp_v1.1, but may be modified by setting the environment variable ABEXP_SCORE_COLUMN.
• A TSV file containing the gene map of the Ensembl gene-IDs to their corresponding gene-names.
  • File name: gene_map.tsv
  • Columns:
    • gene_id
    • gene_name

Development

The project is packaged using poetry.

To install poetry, run:

pipx install poetry

To install the web app, run:

poetry install
# to install the development dependencies
#poetry install --with dev

To set the environment variables, create a .env file in the root of the project. You can simply copy .env.development and rename it to .env.

To set up duckdb:

poetry run flask init-db

To run the web app, run:

poetry run flask run

Deployment

To deploy the app in production, define a .env file with the following variables. Make sure to define the SECRET_KEY variable to something random.

FLASK_ENV=production
SECRET_KEY=<secret_key> # should be something random
DATA_PATH='./data' # the location of the dataset, as defined above
DUCKDB_PATH='./duckdb' # the location where the duckdb will be created
ABEXP_SCORE_COLUMN='abexp_v1.1' # the column name of the abexp-score in the abexp.parquet file

To deploy the app, run:

mkdir duckdb
docker compose up -d

Convert into an apptainer image

Prebuilt image

You can create an apptainer image by following:

apptainer build abexp_web.sif docker-daemon://abexp_web:latest
mkdir duckdb
apptainer exec --bind duckdb:/duckdb:rw --bind example_files:/data:ro abexp_web.sif   sh -c "cd /app; flask init-db && gunicorn abexp_web.wsgi:app -b 0.0.0.0:5000 -w 4"

# other example
apptainer exec --bind duckdb:/duckdb:rw --bind example_files:/data:ro --bind /s/project/abexp_veff/all_variant_combinations/hg38/predict/abexp_v1.1:/data/abexp.parquet/genome=hg38:ro --bind /s/project/abexp_veff/all_variant_combinations/hg19/predict/abexp_v1.1:/data/abexp.parquet/genome=hg19:ro abexp_web.sif sh -c "cd /app; flask init-db && gunicorn abexp_web.wsgi:app -b 0.0.0.0:5000 -w 4"

apptainer exec --bind duckdb:/duckdb:rw --bind example_files:/data:ro abexp_web.sif sh -c "cd /app; flask init-db && gunicorn abexp_web.wsgi:app -b 0.0.0.0:5000 -w 4"