tobiomΒΆ

$ micca tobiom --help
usage: micca tobiom [-h] -i FILE -o FILE [-t FILE] [-s FILE] [-u FILE]

micca tobiom converts the micca OTU table into BIOM Version
1.0 (JSON) format. Optionally, taxonomy and/or sample
information can be added.  When you convert on
(closed-reference) OTU table for PICRUSt, replace OTU IDs with
the original sequence IDs use the option -u/--otuids.

optional arguments:
  -h, --help            show this help message and exit

arguments:
  -i FILE, --input FILE
                        input OTU table file (required).
  -o FILE, --output FILE
                        output BIOM file Version 1.0 (JSON) (required).
  -t FILE, --tax FILE   add taxonomy information from a taxonomy file.
  -s FILE, --sampledata FILE
                        add sample information from a sample data file.
  -u FILE, --otuids FILE
                        replace OTU IDs with the original sequence IDs. Useful
                        when the closed-reference OTU picking protocol was
                        performed for PICRUSt

Example

    micca tobiom -i otutable.txt -o output.biom -t tax.txt -s sampledata.txt