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dcd-mapping

Results

Mapped MaveDB Scoresets can be downloaded here: https://mavedb-mapping.s3.us-east-2.amazonaws.com/mappings.tar.gz

Tool usage

Use the dcd-map command with a scoreset URN, eg

$ dcd-map urn:mavedb:00000083-c-1

Output is saved in the format <URN>_mapping_results.json in the directory specified by the environment variable MAVEDB_STORAGE_DIR, or ~/.local/share/dcd-mapping by default.

Setup

Following installation instructions for CoolSeqTool and Gene Normalizer should take care of the external data dependencies.

Note that Gene Normalizer's pg dependency group must be installed to make use of the PostgreSQL-based backend:

python3 -m pip install 'gene-normalizer[pg]'

Development

Clone the repo

git clone https://github.com/ave-dcd/dcd_mapping
cd dcd_mapping

Create and activate a virtual environment

python3 -m virtualenv venv
source venv/bin/activate

Install as editable and with developer dependencies

python3 -m pip install -e '.[dev,tests]'

Add pre-commit hooks

pre-commit install

When debugging, use flags -c and -d to enable caching of BLAT alignment and debug logging, respectively.