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/v0.15.1/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 0x7f701b3138c0>
-
--password
<password>
¶ Password for BEL Commons
- Default
<function _get_password at 0x7f701b313950>
Arguments
-
path
¶
Required argument