Multiple metrics in a single command (qiime diversity alpha)

User Support
1

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 :slight_smile:
thanks!

2

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

2 Likes
3

and then we need to merge output .tsvs to merged.tsv bleeee, :slight_smile:

4

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

Yeah, after I use more Python to unpack the outputs, merge tables and plot figures.
I learned a lot of Python because of it.

1 Like
5

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/

2 Likes
6

Thanks! I will try it

7

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