make.biom with sample information

Feature requests
1

Hello All,

Would it be possible to add sample data support (e.g., experimental factor, sample collection date, etc) into the “make.biom” command?

Many thanks.
Pedro.

2

Could you post an example of what you would like the resulting biom file to look like?

3

Hi Sarah,

Mothur outputs this:

“columns”:[
{“id”:“sample1”, “metadata”:null},
{“id”:“sample2”, “metadata”:null},
{“id”:“sample3”, “metadata”:null},
{“id”:“sample3”, “metadata”:null},

Could a “metadata” option be added (unless this is what the “groups” does), as in the example below?

“columns”:[
{“id”:“sample1”, “metadata”:{
“site”:“gut”,
“Description”:“human gut”}},
{“id”:“sample2”, “metadata”:{
“other_site”:“soil”,
“Description”:“human gut”}},

4

The groups parameter is used to select samples you would like to include in the biom file. Currently we allow you to provide a *.contaxonomy file to fill metadata with the taxonomy information, but I think it would be fairly easy to add a metadata parameter to allow you to provide more generic data.

Maybe a metadata file like:

sample Tag1 Tag2 …
sampleName info info info …
…

For example:

sample site Description
sample1 “gut” “human gut”
sample2 “soil” “human gut”

Is that what you were thinking?

5

Hello Sarah,

Thanks for your reply. Yes, that is what I had in mind, a file with information to map samples to experimental parameters that can be passed as another option in the “make.biom” command.

Pedro.

6

This will be part of 1.28.0.

7

Great, thanks!