split_otu_table_by_taxonomy.py – Script to split a single OTU table into multiple tables based on the taxonomy at some user-specified depth.

Description:

Usage: split_otu_table_by_taxonomy.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fp

The input otu table in BIOM format

-o, --output_dir

The output directory

-L, --level

The taxonomic level to split at

[OPTIONAL]

--md_identifier

The relevant observation metadat key [default: taxonomy]

--md_as_string

Metadata is included as string [default: metadata is included as list]

Output:

Split seqs_otu_table.biom into taxon-specific OTU tables based on the third level in the taxonomy, and write the taxon-specific OTU tables to ./L3/

split_otu_table_by_taxonomy.py -i otu_table.biom -L 3 -o ./L3/