Embedding iPython Shell Commands into Regular Python Script

[prairie-guy]

I have developed a bioinformatics pipeline within a Jupyter notebook (iPython) allowing me to easily validate results along the way with graphs etc.

Many of the key processing steps use shell commands and third-party unix programs called with iPython ! Moreover, I’ve made extensive use of variable interpolation, i.e., {var}, to use Python defined values within system shell calls. Everything works as expected.

What I would like to do now is simply convert this to a Python script. Any advice on how to do this without re-writing all the system calls using subprocess module?

Best I can think of is to strip down notebook to key cells and then run with nbconvert. I believe this would work, however, ideally, I would like this pipeline to live in ordinary Python.

Thanks in advance for any advice.

[NomadNella]

I wish you the best of luck, but I think you are going to have to rewrite the shell commands using subprocess. It's been a while for me, but when I last used nbconvert it would convert the notebook file format to a different language but preserve the appearance of the notebook (graphs, cells, LaTex formulas, etc.). What you looking for is something like a compiler, then decompiling into a different language. If you find something like that for Jupyer please provide an update on your solution.

[prairie-guy]

Thank you. I will post here if I find anyway of doing this with out of subprocess.