# Multiple metrics in a single command (qiime diversity alpha)
**URL:** https://forum.qiime2.org/t/multiple-metrics-in-a-single-command-qiime-diversity-alpha/13508
**Category:** User Support
**Tags:** diversity
**Created:** [February 6, 2020, 12:19pm UTC](https://forum.qiime2.org/t/multiple-metrics-in-a-single-command-qiime-diversity-alpha/13508 "2020-02-06T12:19:26Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@thedam](https://forum.qiime2.org/u/thedam)
#### Post date: [February 6, 2020, 12:19pm UTC](https://forum.qiime2.org/t/multiple-metrics-in-a-single-command-qiime-diversity-alpha/13508/1 "2020-02-06T12:19:26Z")
Hi, is it possible to run several metrics at once? for example something like:
> ```
> qiime diversity alpha \
> --i-table table.qza \
> --p-metric shannon,observed_otus,goods_coverage \
> --o-alpha-diversity metrics.qza
>
> ```
above doesn't work 🙂
thanks!
---
### Author:  [@lca123](https://forum.qiime2.org/u/lca123)
#### Post date: [February 6, 2020, 1:20pm UTC](https://forum.qiime2.org/t/multiple-metrics-in-a-single-command-qiime-diversity-alpha/13508/2 "2020-02-06T13:20:15Z")
As the following also doesn't work,
```
qiime diversity alpha \
--i-table table.qza \
--p-metric shannon \
--p-metric pielou_e \
--o-alpha-diversity out
```
what I do is a simple bash for loop:
for i in shannon pielou\_e
do
qiime diversity alpha
--i-table table.qza
--p-metric "$i"
--o-alpha-diversity out."$i"
done
---
### Author:  [@thedam](https://forum.qiime2.org/u/thedam)
#### Post date: [February 6, 2020, 1:22pm UTC](https://forum.qiime2.org/t/multiple-metrics-in-a-single-command-qiime-diversity-alpha/13508/3 "2020-02-06T13:22:28Z")
and then we need to merge output .tsvs to merged.tsv bleeee, 🙂
---
### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [February 6, 2020, 1:25pm UTC](https://forum.qiime2.org/t/multiple-metrics-in-a-single-command-qiime-diversity-alpha/13508/4 "2020-02-06T13:25:30Z")
I am using Jupyter lab to combine with Python (I don't know bash commands)
```
variants = ['All', 'Root-Gall', 'Infected']
for variant in variants:
core = 'Data/Core-metrics_analysis/%s_Core-metrics' % variant
outdir = 'Results/Core-metrics_analysis/%s_Core-metrics' % variant
#Alpha diversity comparisons¶
alpha_diversity = ['shannon', 'faith_pd', 'evenness', 'observed_otus']
for alpha in alpha_diversity:
vector = core+'/%s_vector.qza' % alpha
ags_qzv = outdir+'/%s_vector_alpha-group-sign.qzv' % alpha
!qiime diversity alpha-group-significance \
--i-alpha-diversity $vector \
--m-metadata-file Metadata/metadata.tsv \
--o-visualization $ags_qzv
```
> [@thedam](#):
>
> and then we need to merge output .tsvs to merged.tsv bleeee, 🙂
Yeah, after I use more Python to unpack the outputs, merge tables and plot figures.
I learned a lot of Python because of it.
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [February 6, 2020, 1:43pm UTC](https://forum.qiime2.org/t/multiple-metrics-in-a-single-command-qiime-diversity-alpha/13508/5 "2020-02-06T13:43:28Z")
> [@timanix](#):
>
> I am using Jupyter lab to combine with Python (I don’t know bash commands)
Hey @timanix, I suggest you check out the Artifact API, it will provide a much more convenient way for working with QIIME 2 in a python environment:
[https://docs.qiime2.org/2019.10/interfaces/artifact-api/](https://docs.qiime2.org/2019.10/interfaces/artifact-api/)
> [@Moving Pictures Python API tutorial (QIIME2 2018.4)](https://forum.qiime2.org/t/moving-pictures-python-api-tutorial-qiime2-2018-4/4112):
>
> I rewrote the ["Moving Pictures" tutorial using QIIME2 Python API](https://gist.github.com/tkosciol/29de5198a4be81559a075756c2490fde). The original QIIME2 CLI "Moving Pictures" tutorial can be accessed [here](https://docs.qiime2.org/2018.4/tutorials/moving-pictures/). It takes advantage of the latest QIIME2 2018.4 functionalities, especially displaying visualizations in the notebook. You can also [view it in nbviewer](http://nbviewer.jupyter.org/gist/tkosciol/29de5198a4be81559a075756c2490fde). This notebook should be treated as experimental and its goal is to provide a starting point for the users in going from the CLI to Python API. t.
---
### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [February 6, 2020, 2:07pm UTC](https://forum.qiime2.org/t/multiple-metrics-in-a-single-command-qiime-diversity-alpha/13508/6 "2020-02-06T14:07:55Z")
> [@thermokarst](#):
>
> Hey @timanix, I suggest you check out the Artifact API, it will provide a much more convenient way for working with QIIME 2 in a python environment
Thanks! I will try it
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [March 8, 2020, 8:07pm UTC](https://forum.qiime2.org/t/multiple-metrics-in-a-single-command-qiime-diversity-alpha/13508/7 "2020-03-08T20:07:58Z")
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.