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.