Is it worthwhile to have a direct conversion from biomv1 to qiime2 artifact?

Developer Discussion
1

A consistent sore point for users is converting their feature tables to qiime2 artifacts.

It may be easier if we have a transformer that explicitly converts biom table (version 1 text files) to qiime2 artifacts. It shouldn’t be crazy given that the transformer can accept multiple file formats.

To give some context what the current error looks like, when I try to run the following command, I get the following error.

qiime tools import --input-path Microbiomematched.biom --output-path Microbiomematched.qza --type FeatureTable[Frequency]
There was a problem importing Microbiomematched.biom:

  Microbiomematched.biom is not a(n) BIOMV210Format file
2 Likes
2

Like this?

https://docs.qiime2.org/2020.11/tutorials/importing/#biom-v1-0-0

qiime tools import \
  --input-path feature-table-v100.biom \
  --type 'FeatureTable[Frequency]' \
  --input-format BIOMV100Format \
  --output-path feature-table-1.qza

Or do you have something else in mind?

1 Like
3

Yes, that’s exactly what I meant – glad to see it is already implemented in qiime2 :slight_smile:

@quinnr, I think this is the answer to our offline conversation. Do you have anything else you want to add to this?

1 Like
4

Yes. Thanks. I was successfully able to convert from .txt, to .biom to .qza. Of course, I subsequently hit other road block errors with mmvec that I don’t think are related to file conversion.
Plugin error from mmvec:

Nan in summary histogram for: qUbias_1

5

Just as an update, we fixed this problem by filtering out metabolites that are only observed in 1 sample.