Python script for qiime2

Hello everyone,

I have a question in mind.
How to use python in qiime2?
When I write the mentioned question, qiime website is explaining to use the python like the following way, for example:

Usage: summarize_taxa.py [options]

What does that mean? Shouldn’t we write the python script by ourselves?

All the best,
Armin

Hi @ari_sh70,

There’s a two part answer. First, a lot of QIIME 2 is written in python under the hood. You access that through command line scripts in many cases. But, if you want to work with python directly, you can work in the python API. I find this really useful when I want to go between QIIME 2 objects and more specific analyses or I want to do plotting in seaborn. However, I’ll note that that the python API isn’t always well documented.

Best,
Justine

3 Likes

Thank you very much for your reply.
python API seems really nice and I am going to dive into it.

About the first part, I still have some issues. So, how to use through command line? Because I’ve tried to use using command line but it did not work. Can you please explain with an example?

Thanks

Hi @ari_sh70,

This is a QIIME 1 command, and will not work in QIIME 2. Please see the QIIME 2 docs for instructions and examples for QIIME 2:

https://docs.qiime2.org

Thanks @thermokarst That’s what I thought and now I am sure. So, qiime2 hasn’t anymore this ability to use those scripts?

QIIME 2 is a completely new platform, re-designed from the ground up.