metahq retrieve¶

Retrieval commands for tissue, disease, sex, and age annotations.

Usage:

metahq retrieve [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

age¶

Retrieval command for age group annotations.

Usage:

metahq retrieve age [OPTIONS]

Options:

  --terms [fetus|infant|child|adolescent|adult|older_adult|elderly_adult|all]
                                  Age groups to choose. Can combine like
                                  'fetus,adult'.
  --level [sample|series]         GEO annotation level.
  --filters TEXT                  Filters for species, ecode, and technology.
                                  Run `metahq supported` for options.
  --license [permissive|nc|any]   License filter for annotation sources.
                                  'permissive' includes only CC0/CC BY
                                  sources; 'nc' adds non-commercial sources;
                                  'any' includes all sources (default).
  --output PATH                   Path to output directory. Created if it does
                                  not exist; a numeric suffix is appended if
                                  it does.
  --fmt [parquet|tsv|csv|json]
  --metadata TEXT
  --log-level [notset|debug|info|warning|error|critical]
                                  Logging level.
  --quiet                         No log or console output if applied.
  --help                          Show this message and exit.

diseases¶

Retrieval command for disease ontology terms.

Usage:

metahq retrieve diseases [OPTIONS]

Options:

  --terms TEXT
  --level [sample|series]         GEO annotation level.
  --filters TEXT                  Filters for species, ecode, and technology.
                                  Run `metahq supported` for options.
  --license [permissive|nc|any]   License filter for annotation sources.
                                  'permissive' includes only CC0/CC BY
                                  sources; 'nc' adds non-commercial sources;
                                  'any' includes all sources (default).
  --output PATH                   Path to output directory. Created if it does
                                  not exist; a numeric suffix is appended if
                                  it does.
  --fmt [parquet|tsv|csv|json]
  --metadata TEXT
  --mode [annotate|label]         Retrieve annotations or labels.
  --log-level [notset|debug|info|warning|error|critical]
                                  Logging level.
  --quiet                         No log or console output if applied.
  --help                          Show this message and exit.

sex¶

Retrieval command for sex annotations.

Usage:

metahq retrieve sex [OPTIONS]

Options:

  --terms TEXT
  --level [sample|series]         GEO annotation level.
  --filters TEXT                  Filters for species, ecode, and technology.
                                  Run `metahq supported` for options.
  --license [permissive|nc|any]   License filter for annotation sources.
                                  'permissive' includes only CC0/CC BY
                                  sources; 'nc' adds non-commercial sources;
                                  'any' includes all sources (default).
  --output PATH                   Path to output directory. Created if it does
                                  not exist; a numeric suffix is appended if
                                  it does.
  --fmt [parquet|tsv|csv|json]
  --metadata TEXT
  --log-level [notset|debug|info|warning|error|critical]
                                  Logging level.
  --quiet                         No log or console output if applied.
  --help                          Show this message and exit.

tissues¶

Retrieval command for tissue ontology terms.

Usage:

metahq retrieve tissues [OPTIONS]

Options:

  --terms TEXT
  --level [sample|series]         GEO annotation level.
  --filters TEXT                  Filters for species, ecode, and technology.
                                  Run `metahq supported` for options.
  --license [permissive|nc|any]   License filter for annotation sources.
                                  'permissive' includes only CC0/CC BY
                                  sources; 'nc' adds non-commercial sources;
                                  'any' includes all sources (default).
  --output PATH                   Path to output directory. Created if it does
                                  not exist; a numeric suffix is appended if
                                  it does.
  --fmt [parquet|tsv|csv|json]
  --metadata TEXT
  --mode [annotate|label]         Retrieve annotations or labels.
  --log-level [notset|debug|info|warning|error|critical]
                                  Logging level.
  --quiet                         No log or console output if applied.
  --help                          Show this message and exit.