Command Line Interface

biomappings automatically installs the command biomappings. See biomappings --help for usage details.

biomappings

Run the biomappings CLI.

biomappings [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

charts

Make charts.

biomappings charts [OPTIONS]

curate

Run a target curation web app.

biomappings curate [OPTIONS]

Options

--path <path>

Required A predictions TSV file path

export

Create export data file.

biomappings export [OPTIONS]

lint

Sort files and remove duplicates.

biomappings lint [OPTIONS]

Options

--standardize

ndex

Upload to NDEx.

biomappings ndex [OPTIONS]

Options

--username <username>
--password <password>

prune

Prune inferred mappings between the given prefixes from the predictions.

biomappings prune [OPTIONS] [PREFIXES]...

Arguments

PREFIXES

Optional argument(s)

remove-curated

Remove curated mappings from the predicted mappings, use this if they get out of sync.

biomappings remove-curated [OPTIONS]

sssom

Export SSSOM.

biomappings sssom [OPTIONS]

update

Run all update functions.

biomappings update [OPTIONS]

web

Run the biomappings web app.

biomappings web [OPTIONS]

Options

--predictions-path <predictions_path>

A predictions TSV file path

--positives-path <positives_path>

A positives curation TSV file path

--negatives-path <negatives_path>

A negatives curation TSV file path

--unsure-path <unsure_path>

An unsure curation TSV file path