Writing a biom (JSON) file using biomformat package
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grp2009 • 0
@grp2009-11057
Last seen 2.3 years ago

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:

library(biomformat)
otu <- as.data.frame(
    matrix(rpois(9,10),nrow=3)
)
rownames(otu) <- c('OTU1','OTU2','OTU3')
colnames(otu) <- c('Sample1','Sample2','Sample3')
write_biom(make_biom(data=otu),'test.biom')

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?

biomformat json • 998 views
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