================== otu_to_tax_name.py ================== Convert a list of OTU IDs to a list of OTU IDs paired with Genus_species identifiers. .. code-block:: bash usage: otu_to_tax_name.py [-h] -i OTU_ID_FP -t TAXONOMY_FP [-o OUTPUT_FP] Required arguments ^^^^^^^^^^^^^^^^^^ .. cmdoption:: -i OTU_ID_FP, --otu_id_fp OTU_ID_FP Either a text file containing a list (one per line) of OTU IDs, or a tab-separated (classic) BIOM-format file. .. cmdoption:: -t TAXONOMY_FP, --taxonomy_fp TAXONOMY_FP A file associating OTU ID with a full taxonomic specifier. Optional arguments ^^^^^^^^^^^^^^^^^^ .. cmdoption:: -o OUTPUT_FP, --output_fp OUTPUT_FP For a list input, a new file containing a list of OTU IDs and their corresponding short taxonomic identifiers separated by tabs. For a BIOM file input, a new mapping file with all the OTU IDs replaced by the short identifier. .. cmdoption:: -h, --help Show the help message and exit