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.
write_mothur_taxonomy(
obj,
file,
tax_names = obj$get_data("taxon_names")[[1]],
ids = obj$get_data("sequence_id")[[1]],
scores = NULL
)
A taxmap object
(character
of length 1) The file path to save the
sequence fasta file. This is optional.
(character
named by taxon ids) The names of taxa
(character
named by taxon ids) Sequence ids
(numeric
named by taxon ids)
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.;...
Other writers:
make_dada2_asv_table()
,
make_dada2_tax_table()
,
write_greengenes()
,
write_rdp()
,
write_silva_fasta()
,
write_unite_general()