Mapped MaveDB Scoresets can be downloaded here: https://mavedb-mapping.s3.us-east-2.amazonaws.com/mappings.tar.gz
Use the dcd-map command with a scoreset URN, eg
$ dcd-map urn:mavedb:00000083-c-1Output 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.
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]'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.