Question: Writing a biom (JSON) file using biomformat package
gravatar for grp2009
2.5 years ago by
grp20090 wrote:

I am unable to create a biom (JSON, aka BIOM 1.0.0) format file using the biomformat package. Here is my attempt to make a simple biom (JSON) file:

otu <-
rownames(otu) <- c('OTU1','OTU2','OTU3')
colnames(otu) <- c('Sample1','Sample2','Sample3')

The resulting file looks like JSON, but if I run (in the command line)

biom validate-table -i test.biom

I get the error message

AttributeError: 'list' object has no attribute 'lower'

Similarly, other biom convert commands don't work, nor am I able to load this file into phyloseq using its import_biom function. Is this a problem with biomformat, or with the biom program, or with my understanding of the various incompatible BIOM formats?

json biomformat • 744 views
ADD COMMENTlink written 2.5 years ago by grp20090
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 90 users visited in the last hour