Open aguang opened 2 years ago
I think it would be really nice - I had that as a stretch goal at one point. I think it should be possible (probably as a stand-alone package) using HDF5.jl.
One idea I had was, something that reads a .biom
file and can spit out the OTU table and the metadata as separate Tables.jl
- compatible tables, then one could do something like
biom = read_biom("somefile.biom")
cmp = CommunityProfile(otus(biom))
insert!(cmp, metadata(biom))
I think that would be really cool. I will hopefully be bringing on a student to work on some microbiome data I will be getting soon, that might be something we could work on as part of it.
That would be great! It's not a high priority for me to work on on my own, but I'd be more than happy to help someone else with code review / suggestions etc.
Will there be support for the biom format eventually?