Listing [non-]overlapping features

[nick-youngblut]

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

[ebolyen (Evan Bolyen)]

Hi @nick-youngblut!

I’m afraid there’s not really anything analogous in QIIME 2 at the moment. This is definitely something we’ve talked about before though. Usually with the idea that QIIME 2 would understand “axes” and the IDs in a given axis, such as sample/feature/<something we haven’t though of yet!>.

It does strike me that for your particular examples, there might be a way to look at those as metadata (although except for the FeatureData[Taxonomy] we’re missing some stuff to make that happen right away). So maybe there could be some utilities in the q2-metadata plugin which would make a report of the IDs and how they overlap.

I’m going to move this to “Ideas and Suggestions” so others can chime in on this!

Happy New Years!