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"