civic2clinvar
civic2clinvar is a python-based command line utility for extracting CIViC assertions and translating them into ClinVar records.
Installation
$ pip install civic2clinvar
Usage
$ civic2clinvar --help
Usage: civic2clinvar [OPTIONS] ASSERTION_IDS
This command generates a ClinVar-formatted csv file from a specified set
of CIViC assertions.
ASSERTION_IDS are a comma-separated list of assertions, and accepts
integer ranges. Example usage:
civic2clinvar 1,3-5
The above command outputs a ClinVar submission form describing CIViC
assertions 1, 3, 4, and 5 to clinvar.csv (the default output file). Output
destination may be controlled with the --out option, detailed below.
CIViC assertions that are rejected or pending are skipped.
Options:
--aid-file FILENAME Optional file of newline-separated assertion IDs. This
option is mutually exclusive with the ASSERTION_IDS
argument.
-o, --out FILENAME Output file (default: clinvar.csv), use '-' for STDOUT
--help Show this message and exit.