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/v0.15.4/bin/python
pybel [OPTIONS] COMMAND [ARGS]...
Options
- --version¶
Show the version and exit.
- -c, --connection <connection>¶
Database connection string.
- Default
sqlite:////home/docs/.data/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.
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
networks¶
Manage networks.
pybel manage networks [OPTIONS] COMMAND [ARGS]...
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.
- --nodelink <nodelink>¶
Path to output a node-link JSON file.
- --bel <bel>¶
Output canonical BEL.
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 0x7f94007b6290>
- --password <password>¶
Password for BEL Commons
- Default
<function _get_password at 0x7f94007b6320>
Arguments
- path¶
Required argument