Command Line Interface

Note

The command line wrapper might not work on Windows. Use python3 -m pybel if it has issues.

PyBEL automatically installs the command pybel. This command can be used to easily compile BEL documents and convert to other formats. See pybel --help for usage details. This command makes logs of all conversions and warnings to the directory ~/.pybel/.

pybel

PyBEL CLI on /home/docs/checkouts/readthedocs.org/user_builds/pybel/envs/latest/bin/python

pybel [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

-c, --connection <connection>

Database connection string.

Default

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

compile

Compile a BEL script to a graph.

pybel compile [OPTIONS] PATH

Options

--allow-naked-names

Enable lenient parsing for naked names

--disallow-nested

Disable lenient parsing for nested statements

--disallow-unqualified-translocations

Disallow unqualified translocations

--no-identifier-validation

Turn off identifier validation

--no-citation-clearing

Turn off citation clearing

-r, --required-annotations <required_annotations>

Specify multiple required annotations

--upgrade-urls
--skip-tqdm
-v, --verbose

Arguments

PATH

Required argument

insert

Insert a graph to the database.

pybel insert [OPTIONS] path

Arguments

path

Required argument

machine

Get content from the INDRA machine and upload to BEL Commons.

pybel machine [OPTIONS] [AGENTS]...

Options

--local

Upload to local database.

--host <host>

URL of BEL Commons.

Arguments

AGENTS

Optional argument(s)

manage

Manage the database.

pybel manage [OPTIONS] COMMAND [ARGS]...

drop

Drop the database.

pybel manage drop [OPTIONS]

Options

--yes

Confirm the action without prompting.

edges

Manage edges.

pybel manage edges [OPTIONS] COMMAND [ARGS]...
ls

List edges.

pybel manage edges ls [OPTIONS]

Options

--offset <offset>
--limit <limit>

examples

Load examples to the database.

pybel manage examples [OPTIONS]

Options

-v, --debug

namespaces

Manage namespaces.

pybel manage namespaces [OPTIONS] COMMAND [ARGS]...
drop

Drop a namespace by URL.

pybel manage namespaces drop [OPTIONS] URL

Arguments

URL

Required argument

insert

Add a namespace by URL.

pybel manage namespaces insert [OPTIONS] URL

Arguments

URL

Required argument

ls

List cached namespaces.

pybel manage namespaces ls [OPTIONS]

Options

-u, --url <url>

Specific resource URL to list

-i, --namespace-id <namespace_id>

Specific resource URL to list

networks

Manage networks.

pybel manage networks [OPTIONS] COMMAND [ARGS]...
drop

Drop a network by its identifier or drop all networks.

pybel manage networks drop [OPTIONS]

Options

-n, --network-id <network_id>

Identifier of network to drop

-y, --yes

Drop all networks without confirmation if no identifier is given

ls

List network names, versions, and optionally, descriptions.

pybel manage networks ls [OPTIONS]

nodes

Manage nodes.

pybel manage nodes [OPTIONS] COMMAND [ARGS]...
prune

Prune nodes not belonging to any edges.

pybel manage nodes prune [OPTIONS]

summarize

Summarize the contents of the database.

pybel manage summarize [OPTIONS]

neo

Upload to neo4j.

pybel neo [OPTIONS] path

Options

--connection <connection>

Connection string for neo4j upload.

--password <password>

Arguments

path

Required argument

parse

Parse a single BEL statement and pring JSON output.

pybel parse [OPTIONS] TEXT

Options

--pprint

Arguments

TEXT

Required argument

serialize

Serialize a graph to various formats.

pybel serialize [OPTIONS] path

Options

--tsv <tsv>

Path to output a TSV file.

--edgelist <edgelist>

Path to output a edgelist file.

--sif <sif>

Path to output an SIF file.

--gsea <gsea>

Path to output a GRP file for gene set enrichment analysis.

--graphml <graphml>

Path to output a GraphML file. Use .graphml for Cytoscape.

Path to output a node-link JSON file.

--bel <bel>

Output canonical BEL.

Arguments

path

Required argument

summarize

Summarize a graph.

pybel summarize [OPTIONS] path

Arguments

path

Required argument

upload

Upload a graph to BEL Commons.

pybel upload [OPTIONS] path

Options

--host <host>

URL of BEL Commons.

--user <user>

User for BEL Commons

Default

<function _get_user at 0x7f6453ff21e0>

--password <password>

Password for BEL Commons

Default

<function _get_password at 0x7f6453ff2268>

Arguments

path

Required argument

warnings

List warnings from a graph.

pybel warnings [OPTIONS] path

Arguments

path

Required argument