Biom export option that appends taxonomic assignments to the feature table

[vrbana (Alison)]

Would it be possible to have this?

[ebolyen (Evan Bolyen)]

Hey @vrbana,

That’s a very good idea! (we even throw it around every now and then between ourselves)

The way it would work internally (or at least to a plugin developer) is we would create transformers that could accept multiple inputs and produce (multiple?) output formats.

Then it is pretty easy to imangine a transformer that takes BIOM and TSVTaxonomyFormat and returns BIOMWithTaxonomy (just a normal BIOM file really). This would then be easily accessed via the export command.

The bad news is we have a lot of technical debt that still needs to be paid off for those internal components before we can really think about extending them like this. And this isn’t directly related to our push to reach feature parity with QIIME 1 by 2018, so it’s not likely to happen any time soon.

Thanks for the suggestion! We usually prioritize based on user feedback, so this kind of input is really helpful.

[jairideout (Jai Ram Rideout)]

Just a quick note, check out this post for instructions on exporting these data and adding taxonomy info to a .biom file:

Is there any way to summarize taxa plot by category?

Hi @m-ocejo! We currently don’t have that functionality in QIIME 2’s taxa barplots. I created an issue to track the addition of that feature. Note that you can sort the samples by a metadata category, so that samples from the same category will be grouped together (but each bar will still represent a single sample). If you’re interested in using QIIME 1 to produce these grouped barplots, you can export your BIOM table and taxonomy data from your .qza files. In order to use summarize_taxa_throug…

[vrbana (Alison)]

Hi Jai,

This does not currently work. I suspect it is something with the taxonomy output. I noticed it now stops early i.e “k__Bacteria” rather than “k__Bacteria;p__;c__;o__;f__;g__;s” and it has spaces in between each semicolon. If I follow your commands and add my taxonomy to my biom file, I am able to add the taxonomy, but I get the error “TypeError: can only join an iterable” if I try to convert that file to txt and the error “object of type ‘NoneType’ has no len()” if I try to summarize_taxa.py with qiime 1. I have checked and my taxonomy was added correctly to the biom file…

[jairideout (Jai Ram Rideout)]

@vrbana

This does not currently work. I suspect it is something with the taxonomy output. I noticed it now stops early i.e “k__Bacteria” rather than “k__Bacteria;p__;c__;o__;f__;g__;s” and it has spaces in between each semicolon. If I follow your commands and add my taxonomy to my biom file, I am able to add the taxonomy, but I get the error “TypeError: can only join an iterable” if I try to convert that file to txt and the error “object of type ‘NoneType’ has no len()” if I try to summarize_taxa.py with qiime 1. I have checked and my taxonomy was added correctly to the biom file…

@vrbana can you create a new forum topic, and include the exact commands you ran as well as the full error messages? Several users have reported success with that forum topic I linked to, so I'll need more details to figure out what's going on with your data.