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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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readQZA fails #491

Open antagomir opened 5 months ago

antagomir commented 5 months ago

I tried to load example files "distance.qza" and "ordination.qza" from QIIME/DEICODE tutorial.

After downloading them I did in R:

distance.qiime <- mia::readQZA("distance.qza")
ordination.qiime <- mia::readQZA("ordination.qza")

Both throw the error:

Error: Only files in format of 'BIOMV210DirFmt', 'TSVTaxonomyDirectoryFormat', NewickDirectoryFormat' and 'DNASequencesDirectoryFormat' are supported.

-> We might need to add support for more formats? I am not sure how critical feature this is.

antagomir commented 5 months ago

Interestingly, the qiime2R package seems to work. Something to learn from there?

remotes::install_github("jbisanz/qiime2R")
library(qiime2R)
d <- read_qza("distance.qza")
o <- read_qza("ordination.qza")
antagomir commented 2 months ago

We are now adding TSE support for qiime2R; perhaps this solves the issue and we could switch to using qiime2R functions instead of maintaining parallel mia implementation?

This is currently limited by the fact that qiime2R is not available via CRAN or Bioc. There is an open issue on that, however, perhaps the problem will be solved: https://github.com/jbisanz/qiime2R/issues/3

Insaynoah commented 2 months ago

I'll keep an eye on this issue. Might be good to add an example in the book once it's easier to load in qza files and transform them into a tse object.