paxtools 6.0.0.2

Python wrapper for Paxtools.

PAXTools

Python wrapper for Paxtools. This requires Java to run, as this is a pip wrapper for a Java executable jar.

This currently is only a CLI wrapper. This only contains a python utility to convert BioPAX tools to SIF, and fetch inner BioPAX files from a larger file. This satisfies my needs, though I may extend this in the future, and for some time I also plan to review and accept incoming PRs. If this turns out to be a false claim, feel free to email me and I'll gladly move the package name to the motivated individual!

CLI

Running this package directly opens the paxtools jar, which requires Java. JVM arguments can be passed in with the universal environment variable JDK_JAVA_OPTIONS.

Versioning

We care very little about breaking API changes in the actual API, since these largely are reflective of Paxtools changes. Instead, the version is <paxtools-version>.<incremented-number>.

Development

After cloning this repository, run:

git submodule update --init --recursive

which will clone the Paxtools repository under paxtools/paxtools. Install maven, then run mvn install under paxtools/paxtools, which will build the desired (and shadowed!) paxtools/paxtools/paxtools-console/target/paxtools.jar.

The python code under paxtools (cli.py) provides a small installation-invariant wrapper for this tool which can be installed using pip.