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/latest/bin/python Bio2BEL v0.3.9-dev

bio2bel [OPTIONS] COMMAND [ARGS]...

actions

List all actions.

bio2bel actions [OPTIONS]

Options

-c, --connection <connection>

Database connection string.

Default

sqlite:////home/docs/.bio2bel/bio2bel.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/.bio2bel/bio2bel.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/.bio2bel/bio2bel.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/.bio2bel/bio2bel.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/.bio2bel/bio2bel.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
write

Write as BEL Script.

bio2bel main bel write [OPTIONS]

Options

-o, --output <output>
-v, --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/latest/docs/source

-v, --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/latest/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
locate

Print the location of the data directory.

bio2bel main cache locate [OPTIONS]

Options

-v, --verbose
ls

List files in the cache.

bio2bel main cache ls [OPTIONS]

Options

-v, --verbose

drop

Drop the database.

bio2bel main drop [OPTIONS]

Options

-v, --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

summarize

Summarize the contents of the database.

bio2bel main summarize [OPTIONS]

Options

-v, --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/.bio2bel/bio2bel.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/.bio2bel/bio2bel.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/.bio2bel/bio2bel.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/.bio2bel/bio2bel.db

--host <host>
--port <port>