Using the CLI¶

Bio2BEL automatically installs a command line interface with Python’s entry-points. It can be accessed with either python3 -m bio2bel or just as bio2bel from your favorite terminal.

It dynamically loads all Bio2BEL modules installed so commands are aliased.

bio2bel_mirtarbase populate can be accessed as bio2bel mirtarbase populate
bio2bel populate runs all possible repositories’ populate commands.

bio2bel¶

Bio2BEL Command Line Utilities on /home/docs/checkouts/readthedocs.org/user_builds/bio2bel/envs/stable/bin/python Bio2BEL v0.4.1

bio2bel [OPTIONS] COMMAND [ARGS]...

actions¶

List all actions.

bio2bel actions [OPTIONS]

Options

-c, --connection <connection>¶

Database connection string.

Default: sqlite:////home/docs/.data/pybel/pybel_0.14.0_cache.db

bel¶

Manage BEL.

bio2bel bel [OPTIONS] COMMAND [ARGS]...

write¶

Write all as BEL.

bio2bel bel write [OPTIONS]

Options

-c, --connection <connection>¶

Database connection string.

Default: sqlite:////home/docs/.data/pybel/pybel_0.14.0_cache.db

-s, --skip <skip>¶: Modules to skip. Can specify multiple.

-d, --directory <directory>¶: output directory

--force¶: Force overwrite if already exported

belns¶

Manage BEL namespaces.

bio2bel belns [OPTIONS] COMMAND [ARGS]...

write¶

Write a BEL namespace names/identifiers to terminology store.

bio2bel belns write [OPTIONS]

Options

-c, --connection <connection>¶

Database connection string.

Default: sqlite:////home/docs/.data/pybel/pybel_0.14.0_cache.db

-s, --skip <skip>¶: Modules to skip. Can specify multiple.

-d, --directory <directory>¶: output directory

-f, --force¶: Force re-download and re-population of resources

cache¶

Manage caches.

bio2bel cache [OPTIONS] COMMAND [ARGS]...

clear¶

Clear all caches.

bio2bel cache clear [OPTIONS]

Options

-s, --skip <skip>¶: Modules to skip. Can specify multiple.

drop¶

Drop all

bio2bel drop [OPTIONS]

Options

Drop all?¶: Confirm the action without prompting.

-c, --connection <connection>¶

Database connection string.

Default: sqlite:////home/docs/.data/pybel/pybel_0.14.0_cache.db

-s, --skip <skip>¶: Modules to skip. Can specify multiple.

er¶

Generate entity-relation diagrams for each package.

bio2bel er [OPTIONS]

Options

-d, --directory <directory>¶

install¶

Install the Bio2BEL package.

bio2bel install [OPTIONS] NAME

Arguments

NAME¶: Required argument

main¶

# Manage pid.pathways

bio2bel main [OPTIONS] COMMAND [ARGS]...

Options

-c, --connection <connection>¶

Default: sqlite:////home/docs/.data/pybel/pybel_0.14.0_cache.db

bel¶

Manage BEL.

bio2bel main bel [OPTIONS] COMMAND [ARGS]...

upload¶

Upload BEL to BEL Commons.

bio2bel main bel upload [OPTIONS]

Options

--host <host>¶: URL of BEL Commons.

-v, --verbose¶: Enable verbose mode. More -v’s means more verbose.

write¶

Write as BEL Script.

bio2bel main bel write [OPTIONS]

Options

-o, --output <output>¶

-v, --verbose¶: Enable verbose mode. More -v’s means more verbose.

write-edgelist¶

Write as an edge list and node list file.

bio2bel main bel write-edgelist [OPTIONS]

Options

-d, --directory <directory>¶

output directory, defaults to current.

Default: /home/docs/checkouts/readthedocs.org/user_builds/bio2bel/checkouts/stable/docs/source

-v, --verbose¶: Enable verbose mode. More -v’s means more verbose.

belns¶

Manage BEL namespace.

bio2bel main belns [OPTIONS] COMMAND [ARGS]...

drop¶

Clear names/identifiers to terminology store.

bio2bel main belns drop [OPTIONS]

upload¶

Upload names/identifiers to terminology store.

bio2bel main belns upload [OPTIONS]

Options

-u, --update¶

write¶

Write a BEL namespace names/identifiers to terminology store.

bio2bel main belns write [OPTIONS]

Options

-d, --directory <directory>¶

output directory, defaults to current.

Default: /home/docs/checkouts/readthedocs.org/user_builds/bio2bel/checkouts/stable/docs/source

cache¶

Manage cached data.

bio2bel main cache [OPTIONS] COMMAND [ARGS]...

clear¶

Clear all files from the cache.

bio2bel main cache clear [OPTIONS]

Options

-v, --verbose¶: Enable verbose mode. More -v’s means more verbose.

locate¶

Print the location of the data directory.

bio2bel main cache locate [OPTIONS]

Options

-v, --verbose¶: Enable verbose mode. More -v’s means more verbose.

ls¶

List files in the cache.

bio2bel main cache ls [OPTIONS]

Options

-v, --verbose¶: Enable verbose mode. More -v’s means more verbose.

drop¶

Drop the database.

bio2bel main drop [OPTIONS]

Options

-v, --verbose¶: Enable verbose mode. More -v’s means more verbose.

--yes¶: Confirm the action without prompting.

export-gene-sets¶

Export all pathway - gene info to a excel file.

bio2bel main export-gene-sets [OPTIONS]

Options

-d, --directory <directory>¶: Defaults to CWD

-f, --fmt <fmt>¶

Default: excel
Options: xlsx|tsv

populate¶

Populate the database.

bio2bel main populate [OPTIONS]

Options

-r, --reset¶: Nuke database first

-f, --force¶: Force overwrite if already populated

-v, --verbose¶: Enable verbose mode. More -v’s means more verbose.

summarize¶

Summarize the contents of the database.

bio2bel main summarize [OPTIONS]

Options

-v, --verbose¶: Enable verbose mode. More -v’s means more verbose.

web¶

Run the web app.

bio2bel main web [OPTIONS]

Options

-v, --debug¶

-p, --port <port>¶

-h, --host <host>¶

-k, --secret-key <secret_key>¶

populate¶

Populate all.

bio2bel populate [OPTIONS]

Options

-c, --connection <connection>¶

Database connection string.

Default: sqlite:////home/docs/.data/pybel/pybel_0.14.0_cache.db

--reset¶: Nuke database first

--force¶: Force overwrite if already populated

-s, --skip <skip>¶: Modules to skip. Can specify multiple.

sheet¶

Generate a summary sheet.

bio2bel sheet [OPTIONS]

Options

-c, --connection <connection>¶

Database connection string.

Default: sqlite:////home/docs/.data/pybel/pybel_0.14.0_cache.db

-s, --skip <skip>¶: Modules to skip. Can specify multiple.

-f, --file <file>¶

--tablefmt <tablefmt>¶

Default: simple

--index¶

summarize¶

Summarize all.

bio2bel summarize [OPTIONS]

Options

-c, --connection <connection>¶

Database connection string.

Default: sqlite:////home/docs/.data/pybel/pybel_0.14.0_cache.db

-s, --skip <skip>¶: Modules to skip. Can specify multiple.

web¶

Run a combine web interface.

bio2bel web [OPTIONS]

Options

-c, --connection <connection>¶

Database connection string.

Default: sqlite:////home/docs/.data/pybel/pybel_0.14.0_cache.db

--host <host>¶

--port <port>¶