Parse a BIOM output from QIIME
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")
characterof 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
parse_tax_datafor examples of how this works.
characterof length 1) The identity of the capturing groups defined using
class_regex. The length of
class_keymust 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
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 http://geoffreyzahn.com/getting-your-otu-table-into-r/.
A taxmap object