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