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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/

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