Usage

This package provides a command line interface.

To run the Normalizer on a description variant:

$ mutalyzer_normalizer "NG_012337.1(NM_003002.2):c.274G>T"

Enable the file based cache

Create a cache directory and a configuration file:

$ mkdir cache
$ echo MUTALYZER_CACHE_DIR = $(pwd)/cache > config.txt

Setup the email address used to communicate with the NCBI:

$ echo EMAIL = your.email@address.com >> config.txt

Optionally, setup the NCBI API key:

$ echo NCBI_API_KEY = your_NCBI_key >> config.txt

Populate the cache:

$ mutalyzer_retriever --id NC_000022.11 --parse --split --output cache

Now the tool can be run with the cache:

$ MUTALYZER_SETTINGS="$(pwd)/config.txt" mutalyzer_normalizer "NC_000022.11(NM_182984.5):c.95del"