parse_qiime_biom: Parse a BIOM output from QIIME

Description Usage Arguments Details Value See Also

View source: R/parsers.R


Parses a file in BIOM format from QIIME into a taxmap object. This also seems to work with files from MEGAN. I have not tested if it works with other BIOM files.


parse_qiime_biom(file, class_regex = "(.*)", class_key = "taxon_name")



(character of length 1) The file path to the input file.


A regular expression used to parse data in the taxon names. There must be a capture group (a pair of parentheses) for each item in class_key. See parse_tax_data for examples of how this works.


(character of length 1) The identity of the capturing groups defined using class_regex. The length of class_key must be equal to the number of capturing groups specified in class_regex. Any names added to the terms will be used as column names in the output. At least one "taxon_name" must be specified. Only "info" can be used multiple times. Each term must be one of those described below:

  • taxon_name: The name of a taxon. Not necessarily unique, but are interpretable by a particular database. Requires an internet connection.

  • taxon_rank: The rank of the taxon. This will be used to add rank info into the output object that can be accessed by out$taxon_ranks().

  • info: Arbitrary taxon info you want included in the output. Can be used more than once.


This function was inspired by the tutorial created by Geoffrey Zahn at


A taxmap object

See Also

Other parsers: parse_edge_list, parse_greengenes, parse_mothur_tax_summary, parse_mothur_taxonomy, parse_newick, parse_phyloseq, parse_phylo, parse_rdp, parse_silva_fasta, parse_ubiome, parse_unite_general

grunwaldlab/metacoder documentation built on Oct. 2, 2018, 10:25 p.m.