pybel-cx 0.1.0

A PyBEL extension for interconversion with CX

A PyBEL extension for interconversion with CX

Installation

Before this is deployed to PyPI, it can be installed with:

$ python3 -m pip install git+https://github.com/pybel/pybel-cx.git

Command Line Usage

PyBEL-CX installs two command line utilities: bel_to_cx and cx_to_bel.

CX to BEL

Running this script has the caveat that the CX document should conform to the schema created by PyBEL-CX.

$ cat my_network.cx | cx_to_bel > my_network.bel

BEL to CX

$ cat my_network.bel | bel_to_cx > my_network.cx

Since this operation can be expensive, PyBEL caches namespace resources. The -c flag can be used to specify a database connection string to use a high performance RDBMS instead of the default SQLite. For example, if you would like to use MySQL, this database string will look something like mysql+pymysql://<username>:<password>@<host>/<dbname>?charset=utf8[&<options>]. Be sure to pip install the connector, which is pymysql in this example.

$ pip install pymysql
$ cat my_network.bel | bel_to_cx -c "mysql+pymysql://root:root@localhost/mydb?charset=utf8" > my_network.cx

More documentation on connection strings at http://pybel.readthedocs.io/en/latest/manager.html#pybel.manager.BaseManager.from_connection.