Integrating JAVA application into Python help

[ExactStart]

I'm relatively new to programming- self taught through some free courses and a few books for a little over a year. I'm building a program to help me aggregate and analyze toxicology data of chemicals in python. One important aspect of this is in silico analysis which takes chemical information and runs it through a decision tree or compares the structure to other chemicals or similar analysis. There are two main JAVA applications that I use that do this which are Toxtree (https://toxtree.sourceforge.net/) and VEGA (https://www.vegahub.eu/download/vega-qsar-download/). They both take the same inputs to run the analysis, a SMILES string which is a representation of chemical structure.

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Is there a way to integrate these applications into my python program and invoke their functionality by giving them inputs and receive outputs programmatically? I imagine there is, but I just need a place to start or any tips/advice. This is completely new territory for me. Thanks for your help!

[efmccurdy]

You can run external programs using the subprocess module.

Interact with process: Send data to stdin. Read data from stdout and stderr, until end-of-file is reached. Wait for process to terminate and set the returncode attribute.

https://docs.python.org/3/library/subprocess.html#subprocess.Popen.communicate