I've created the following artifacts via the following methods:
OTU abundances .tsv file --> biom --> FeatureTable[Frequency]
taxonomy .tsv file --> FeatureData[Taxonomy]
tree .nwk file --> Phylogeny[Rooted]
Now that I've converted all of the data to artifacts, is there a method directly available in qiime for checking that the sample/feature IDs imported correctly and all of the IDs overlap between the artifacts? Given that at least for some qiime commands, there's no warning if sample/feature IDs don't overlap (samples/features are just silently filtered), I want to make sure all of my artifacts match. In R, one could do this with the setdiff()
& intersect()
functions, but I don't see anything equivalent in qiime2. Am I missing it?
System versions
Python version: 3.5.4
QIIME 2 release: 2017.10
QIIME 2 version: 2017.10.0
q2cli version: 2017.10.0
Installed plugins
alignment 2017.10.0
composition 2017.10.0
dada2 2017.10.0
deblur 2017.10.0
demux 2017.10.0
diversity 2017.10.0
emperor 2017.10.0
feature-classifier 2017.10.0
feature-table 2017.10.0
gneiss 2017.10.0
longitudinal 2017.10.0
metadata 2017.10.0
phylogeny 2017.10.0
quality-control 2017.10.0
quality-filter 2017.10.0
sample-classifier 2017.10.0
taxa 2017.10.0
types 2017.10.0
vsearch 2017.10.0