Parse a BIOM format file and obtain a list of unique OTUIDs found in each category in mapping file.

usage: extract_uniques.py [-h] [-p PREFIX] input_biom_fp output_dir mapping_file category_column

Required arguments


BIOM format file path.


Mapping file with category information.


Column in mapping file specifying the category/condition of all samples.

Optional arguments

-o OUTPUT_DIR, --output_dir OUTPUT_DIR

Path to save category unique OTUIDs.

-p PREFIX, --prefix PREFIX

Provide specific text to prepend the output file names. By default, the ‘unique’ will be added in front of output filenames.

-r REVERSE, --reverse REVERSE

Get shared OTUIDs among all unique combinations of groups and write out the results to path provided to this option.

-h, --help

Show the help message and exit