Biom files for shiny_phyloseq

Integrating mothur with other programs
1

Has anyone had experience using .biom files from mothur with phyloseq?

I created a .biome file using a .shared and .constaxonomy files. The .biome file wouldn’t upload successful into shiny-phyloseq and phyloseq wouldn’t import it either. Here is the error output: Error in validObject(.Object) :
invalid class “otu_table” object: superclass “vector_OR_factor” not defined in the environment of the object’s class

I tried converting the mothur .biom file to newer json and hdf5 formats, and no luck there either.

Any thoughts?

2

I usually just import mothur files into phyloseq using phyloseqs import_mothur function.

Cheers
Richard

4

Hello Richard,

I agree one can use import function in phyloseq for importing mothur files.
However the major issue is with phylogenetic tree generated from mothur.

example
mothur_ps = import_mothur(mothur_list_file = "test_list.list", mothur_group_file = NULL, mothur_tree_file = NULL, cutoff = NULL, mothur_shared_file = "test.shared", mothur_constaxonomy_file = "test.0.03.cons.taxonomy", parseFunction = parse_taxonomy_default)

#Add in phylogenetic
phy.tre = read_tree_greengenes("test.phylip.tre")

ntaxa(phy.tre)
[1] 510
taxa_names(mothur_ps)
[1] M00967_43_000000000-A3JHG_1_1101_17289_26831 (like this)

I don’t know how to resolve this problem? how can we generate Phyloseq compatible Phylip file?

Thank you in advance

5

Hi Richard,

I have found the solution to it. I just added OTU information to the sequence IDs

Thanks