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-phenotype-links
Create links between gene and phenotype.
clinvar-this data gene-phenotype-links [OPTIONS] INPUT_FILE OUTPUT_FILE
Options
- --needs-hpo-terms, --no-needs-hpo-terms
Whether to filter to rows with HPO terms (default: true)
Arguments
- INPUT_FILE
Required argument
- OUTPUT_FILE
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