Scroll to navigation

PYBEL(1) User Commands PYBEL(1)

NAME

pybel - Command line interface for PyBEL

SYNOPSIS

pybel [OPTIONS] COMMAND [ARGS]...

DESCRIPTION


PyBEL is a pure Python package for parsing and handling biological
networks encoded in the Biological Expression Language (BEL) version
2. It also facilitates data interchange between common formats and
databases such as NetworkX, JSON, CSV, SIF, Cytoscape, CX, NDEx, SQL,
and Neo4J.

OPTIONS

Show the version and exit.
Database connection string. [default: sqlite:////home/andreas/.pybel/pybel_0.14.0_cache.db]
Show this message and exit.

Commands:

Compile a BEL script to a graph.
Insert a graph to the database.
Get content from the INDRA machine and upload to BEL Commons.
Manage the database.
Upload to neo4j.
Upload a graph to BEL Commons.
Serialize a graph to various formats.
Summarize a graph.
List warnings from a graph.

AUTHOR


This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.

March 2020 pybel 0.14.5