Attempts to save taxonomic and sequence information of a taxmap object in the
RDP FASTA format. If the taxmap object was created using
parse_rdp
, then it should be able to replicate the format
exactly with the default settings.
write_rdp(
obj,
file,
tax_names = obj$get_data("taxon_names")[[1]],
ranks = obj$get_data("rdp_rank")[[1]],
ids = obj$get_data("rdp_id")[[1]],
info = obj$get_data("seq_name")[[1]],
sequences = obj$get_data("rdp_seq")[[1]]
)
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) The ranks of taxa
(character
named by taxon ids) Sequence ids
(character
named by taxon ids) Info associated with
sequences. In the example output shown here, this field corresponds to
"Sparassis crispa; MBUH-PIRJO&ILKKA94-1587/ss5"
(character
named by taxon ids) Sequences
The output file has a format like:
>S000448483 Sparassis crispa; MBUH-PIRJO&ILKKA94-1587/ss5 Lineage=Root;rootrank;Fun...
ggattcccctagtaactgcgagtgaagcgggaagagctcaaatttaaaatctggcggcgtcctcgtcgtccgagttgtaa
tctggagaagcgacatccgcgctggaccgtgtacaagtctcttggaaaagagcgtcgtagagggtgacaatcccgtcttt
...
Other writers:
make_dada2_asv_table()
,
make_dada2_tax_table()
,
write_greengenes()
,
write_mothur_taxonomy()
,
write_silva_fasta()
,
write_unite_general()