Command Line Interface

clinvar-this

Main entry point for CLI via click.

clinvar-this [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

--verbose, --no-verbose
--profile <profile>

The profile to use

--verify-ssl, --no-verify-ssl

Whether to enable SSL verification

batch

Sub comment category batch ...

clinvar-this batch [OPTIONS] COMMAND [ARGS]...

export

Export batch data to a given file

clinvar-this batch export [OPTIONS] NAME PATH

Options

--force, --no-force

Overwrite existing files

--struc-var, --no-struc-var

Export structural variants rather than sequence variants

Arguments

NAME

Required argument

PATH

Required argument

import

Import data for a new or existing batch

clinvar-this batch import [OPTIONS] PATH

Options

-m, --metadata <metadata>

Provide meta data settings as KEY=VALUE settings

--name <name>

Name of the batch to create or add to

Arguments

PATH

Required argument

list

List existing batches

clinvar-this batch list [OPTIONS]

retrieve

Submit the given batch to ClinVar

clinvar-this batch retrieve [OPTIONS] NAME

Options

--use-testing, --no-testing

Whether to use the testing API

Arguments

NAME

Required argument

submit

Submit the given batch to ClinVar

clinvar-this batch submit [OPTIONS] NAME

Options

--use-testing, --no-testing

Whether to use the testing API

--dry-run, --no-dry-run

Whether to use the ClinVar dry-run

Arguments

NAME

Required argument

update-metadata

Update batch metadata without importing files

clinvar-this batch update-metadata [OPTIONS] NAME [METADATA]...

Arguments

NAME

Required argument

METADATA

Optional argument(s)

config

Sub command category varfish-this config ...

clinvar-this config [OPTIONS] COMMAND [ARGS]...

dump

Sub command varfish-this config dump

Print the configuration file to stdout.

clinvar-this config dump [OPTIONS]

get

Sub command varfish-this config get NAME

Show the configuration variable with the given NAME. This will interpret the current --profile setting.

clinvar-this config get [OPTIONS] NAME

Options

--profile <profile>

The profile to get the value from

Arguments

NAME

Required argument

set

Sub command varfish-this config set NAME VALUE

Set the configuration variable with the given NAME to the given VALUE. This will interpret the current --profile setting.

clinvar-this config set [OPTIONS] NAME VALUE

Arguments

NAME

Required argument

VALUE

Required argument

data

Sub command category “data”.

clinvar-this data [OPTIONS] COMMAND [ARGS]...

acmg-class-by-freq

Create links between gene and phenotype.

clinvar-this data acmg-class-by-freq [OPTIONS] INPUT_FILE OUTPUT_FILE

Options

--thresholds <thresholds>

Whether to filter to rows with HPO terms (default: true)

Arguments

INPUT_FILE

Required argument

OUTPUT_FILE

Required argument

extract-vars

Write out variants from RCV records.

clinvar-this data extract-vars [OPTIONS] PATH_INPUT PATH_OUTPUT_DIR

Options

--gzip-output, --no-gzip-output

Whether to gzip output (default: true)

Arguments

PATH_INPUT

Required argument

PATH_OUTPUT_DIR

Required argument

gene-variant-report

Create a gene variant summary report.

clinvar-this data gene-variant-report [OPTIONS] INPUT_FILE OUTPUT_FILE

Arguments

INPUT_FILE

Required argument

OUTPUT_FILE

Required argument

xml-to-jsonl

Convert XML to JSONL

clinvar-this data xml-to-jsonl [OPTIONS] INPUT_FILE OUTPUT_FILE

Options

--max-records <max_records>

Maximum number of records to convert

Arguments

INPUT_FILE

Required argument

OUTPUT_FILE

Required argument