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divbase-cli dimensions

Create and inspect dimensions (number of samples, number of variants, scaffold names) of the VCF files in a project

Usage:

$ divbase-cli dimensions [OPTIONS] COMMAND [ARGS]...

Options:

  • --install-completion: Install completion for the current shell.
  • --show-completion: Show completion for the current shell, to copy it or customize the installation.
  • --help: Show this message and exit.

Commands:

  • update: Calculate and add the dimensions of a VCF...
  • show: Show the dimensions index file for a project.
  • create-metadata-template: Create a template sample metadata file...
  • validate-metadata-file: Validate a sample metadata TSV file...

divbase-cli dimensions update

Calculate and add the dimensions of a VCF file to the dimensions index file in the project.

Usage:

$ divbase-cli dimensions update [OPTIONS]

Options:

  • -p, --project TEXT: Name of the DivBase project, if not provided uses the default in your DivBase config file
  • --help: Show this message and exit.

divbase-cli dimensions show

Show the dimensions index file for a project. When running --unique-scaffolds, the sorting separates between numeric and non-numeric scaffold names.

Usage:

$ divbase-cli dimensions show [OPTIONS]

Options:

  • --filename TEXT: If set, will show only the entry for this VCF filename.
  • --unique-scaffolds: If set, will show all unique scaffold names found across all the VCF files in the project.
  • --unique-samples: If set, will show all unique sample names found across all the VCF files in the project.
  • --sample-names-limit INTEGER RANGE: Maximum number of sample names to display per list in terminal output. [default: 20; x>=1]
  • --sample-names-output TEXT: Write full sample names to file instead of truncating in terminal output. Mutually exclusive with --sample-names-stdout.
  • --sample-names-stdout: Print full sample names to stdout (useful for piping). Mutually exclusive with --sample-names-output.
  • -p, --project TEXT: Name of the DivBase project, if not provided uses the default in your DivBase config file
  • --help: Show this message and exit.

divbase-cli dimensions create-metadata-template

Create a template sample metadata file (TSV format) pre-filled with the sample names from the project's VCF files based on the information stored in the project's VCF dimensions cache. Tip: run 'divbase-cli dimensions update' first to ensure that the VCF dimensions areup-to-date.

Usage:

$ divbase-cli dimensions create-metadata-template [OPTIONS]

Options:

  • -o, --output FILE: Path to the output TSV file to create. Defaults to sample_metadata_<project_name>.tsv in the current directory. If a file already exists at the given path, you will be prompted to confirm if you want to overwrite it.
  • -p, --project TEXT: Name of the DivBase project, if not provided uses the default in your DivBase config file
  • --help: Show this message and exit.

divbase-cli dimensions validate-metadata-file

Validate a sample metadata TSV file (before you upload it to the project's data store) to check that it will work with DivBase queries.

Usage:

$ divbase-cli dimensions validate-metadata-file [OPTIONS] INPUT_PATH

Arguments:

  • INPUT_PATH: Path to the input TSV file to validate. [required]

Options:

  • --untruncated: Show full (untruncated) validator lists (including sample mismatches and grouped warning row/value previews).
  • -p, --project TEXT: Name of the DivBase project, if not provided uses the default in your DivBase config file
  • --help: Show this message and exit.