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