Command-line interface (CLI)#

OpenVariant is a package that can be run in Python scripts, but, also, allow to the user to run some of its tasks in a shell and command language. The same tasks that can be executed through a command-line interface (CLI) that we present here can be also performed in a Python script.

The main command that rules OpenVariant is openvar, with that command we can choose different options to perform different tasks. The tasks with their parameters are the following ones:

$ 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#

Concatenate parsed files on the standard output. For these options the parameters are the following ones:

input_path - Input path.
-w,--where - Condition expression.
-a,--annotations - Annotation path.
--header - Show headers on the result.
--skip - Skip unreadable files and directories.

# Example
openvar cat /project/datasets -w "SCORE >= 5" -a /project/annotation.yaml  --header --skip

Count command#

Number of rows that matches a specific condition. The parameters are the following ones:

input_path - Input path.
-w,--where - Condition expression.
-g,--group_by - Key to group rows.
-a,--annotations - Annotation path.
-c,--cores - Maximum processes to run in parallel.
-q,--quite - Don’t show the progress.
--skip - Skip unreadable files and directories.

# Example
openvar count /project/datasets -w "REF >= 5034" -g COUNTRY -a /project/annotation.yaml -c 10 -q --skip

Group by command#

Number of rows that matches a specific condition. The parameters are the following ones:

input_path - Input path.
-w,--where - Condition expression.
-g,--group_by - Key to group rows.
-a,--annotations - Annotation path.
-c,--cores - Maximum processes to run in parallel.
-q,--quite - Don’t show the progress.
--skip - Skip unreadable files and directories.

# Example
openvar count /project/datasets -w "REF >= 5034" -g COUNTRY -a /project/annotation.yaml -c 10 -q --skip

Plugin command#

Actions to apply on the plugins system. Mainly create the template of a new plugin. For that, these parameters can be used (to learn more about how plugins work, check Plugin system section):

action - Action to perform [‘create’].
-n,--name - Name of the plugin.
-d,--directory - Directory path where plugin is or will be located.

Create#

It will generate the template with required files to apply and run a new plugin with the name stipulated and in the default directory.

# Example
openvar plugin create -n reverse_value

For further details, check Command-line interface (CLI) examples and you will have a clearer picture on how to use CLI tasks.

Tasks

Plugin system