Introduction#

OpenVariant offers a command-line interface (CLI) with the main tasks that also can be applied in Python scripts.

On the following command you can check the different options that openvar can run.

[1] -

%%bash
openvar --help

Usage: openvar [OPTIONS] COMMAND [ARGS]...

  'openvar' is the command-line interface of OpenVariant. Parsing and data
  transformation of multiple input formats.

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  cat      Concatenate parsed files to standard output.
  count    Number of rows that matches a specified criterion.
  groupby  Group the parsed result for each different value of the specified
           key.
  plugin   Actions to execute for a plugin: create.

Cat command#

[1] -

%%bash
openvar cat --help

Usage: openvar cat [OPTIONS] [INPUT_PATH]

  Print the parsed files on the stdout/"output".

Options:
  -w, --where TEXT        Filter expression. eg: CHROMOSOME == 4
  -a, --annotations PATH  Annotation path. eg: /path/annotation_vcf.yaml
  --header                Show the result header.
  -o, --output TEXT       File to write the output.
  --skip                  Skip files and directories that are unreadable.
  -h, --help              Show this message and exit.

Count command#

[2] -

%%bash
openvar count --help

Usage: openvar count [OPTIONS] [INPUT_PATH]

  Print on the stdout/"output" the number of rows that meets the criteria.

Options:
  -w, --where TEXT        Filter expression. eg: CHROMOSOME == 4
  -g, --group_by TEXT     Key to group rows. eg: COUNTRY
  -a, --annotations PATH  Annotation path. eg: /path/annotation_vcf.yaml
  -c, --cores INTEGER     Maximum processes to run in parallel.
  -q, --quite             Don't show the progress.
  -o, --output TEXT       File to write the output.
  --skip                  Skip files and directories that are unreadable.
  -h, --help              Show this message and exit.

Group by command#

[3] -

%%bash
openvar groupby --help

Usage: openvar groupby [OPTIONS] [INPUT_PATH]

  Print on the stdout/"output" the parsed files group by a specified field.

Options:
  --header                Show the result header.
  --show                  Show group by each row.
  -w, --where TEXT        Filter expression. eg: CHROMOSOME == 4
  -g, --group_by TEXT     Key to group rows. eg: COUNTRY
  -s, --script TEXT       Filter expression. eg: gzip >
                          \${GROUP_KEY}.parsed.tsv.gz
  -a, --annotations PATH  Annotation path. eg: /path/annotation_vcf.yaml
  -c, --cores INTEGER     Maximum processes to run in parallel.
  -q, --quite             Don't show the progress.
  -o, --output TEXT       File to write the output.
  --skip                  Skip files and directories that are unreadable.
  -h, --help              Show this message and exit.

Plugin command#

[4] -

%%bash
openvar plugin --help

Usage: openvar plugin [OPTIONS] {create}

  Actions to apply on the plugin system.

Options:
  -n, --name TEXT  Name of the plugin.
  -h, --help       Show this message and exit.

Command-line interface (CLI) examples

Main tasks