otu_to_tax_name.py

Convert a list of OTU IDs to a list of OTU IDs paired with Genus_species identifiers.

usage: otu_to_tax_name.py [-h] -i OTU_ID_FP -t TAXONOMY_FP [-o OUTPUT_FP]

Required arguments

-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.

-t TAXONOMY_FP, --taxonomy_fp TAXONOMY_FP

A file associating OTU ID with a full taxonomic specifier.

Optional arguments

-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.

-h, --help

Show the help message and exit