The Amissense Tool analyzes and visualizes AlphaMissense pathogenicity scores, integrating AlphaFold structures and ClinVar data. It offers automated pipelines, visualizations, and versatile command-line utilities.
Description:
The load_config() function currently assumes that config.json is always located in the Amissense directory. It would be more flexible to allow the path to config.json to be specified via an environment variable or as a command-line argument. This would make the configuration more adaptable to different environments.
Proposed Solution:
Add support for an environment variable (e.g., AMISSENSE_CONFIG_PATH) to specify the path to the config.json file.
Modify the command-line interface to accept a --config-path argument, which can override the default config path.
Description:
The
load_config()function currently assumes thatconfig.jsonis always located in theAmissensedirectory. It would be more flexible to allow the path toconfig.jsonto be specified via an environment variable or as a command-line argument. This would make the configuration more adaptable to different environments.Proposed Solution:
AMISSENSE_CONFIG_PATH) to specify the path to theconfig.jsonfile.--config-pathargument, which can override the default config path.