write_mothur_taxonomy: Write an imitation of the Mothur taxonomy file

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Write an imitation of the Mothur taxonomy file

Description

Attempts to save taxonomic information of a taxmap object in the mothur '*.taxonomy' format. If the taxmap object was created using parse_mothur_taxonomy, then it should be able to replicate the format exactly with the default settings.

Usage

write_mothur_taxonomy(
  obj,
  file,
  tax_names = obj$get_data("taxon_names")[[1]],
  ids = obj$get_data("sequence_id")[[1]],
  scores = NULL
)

Arguments

obj	A taxmap object
file	(character of length 1) The file path to save the sequence fasta file. This is optional.
tax_names	(character named by taxon ids) The names of taxa
ids	(character named by taxon ids) Sequence ids
scores	(numeric named by taxon ids)

Details

The output file has a format like:

AY457915	Bacteria(100);Firmicutes(99);Clostridiales(99);Johnsone...
AY457914	Bacteria(100);Firmicutes(100);Clostridiales(100);Johnso...
AY457913	Bacteria(100);Firmicutes(100);Clostridiales(100);Johnso...
AY457912	Bacteria(100);Firmicutes(99);Clostridiales(99);Johnsone...
AY457911	Bacteria(100);Firmicutes(99);Clostridiales(98);Ruminoco...

or...

AY457915	Bacteria;Firmicutes;Clostridiales;Johnsonella_et_rel.;J...
AY457914	Bacteria;Firmicutes;Clostridiales;Johnsonella_et_rel.;J...
AY457913	Bacteria;Firmicutes;Clostridiales;Johnsonella_et_rel.;J...
AY457912	Bacteria;Firmicutes;Clostridiales;Johnsonella_et_rel.;J...
AY457911	Bacteria;Firmicutes;Clostridiales;Ruminococcus_et_rel.;...

See Also

Other writers: make_dada2_asv_table(), make_dada2_tax_table(), write_greengenes(), write_rdp(), write_silva_fasta(), write_unite_general()

metacoder documentation built on April 4, 2023, 9:08 a.m.