BUG: Update summarize_otu_by_cat.py to use biom 2.x

I've updated the script and added a new script usage case.

See #1713
Is this supposed to be `axis='sample'`? The script docs say "Normalize OTU counts, where the OTU table columns sum to 1". I think normalizing by sample will achieve this (see the BIOM [doctest examples](http://biom-format.org/documentation/generated/biom.table.Table.norm.html#biom.table.Table.norm)).