Attempts to save taxonomic and sequence information of a taxmap object in the
Greengenes output format. If the taxmap object was created using
parse_greengenes
, then it should be able to replicate the
format exactly with the default settings.
write_greengenes(
obj,
tax_file = NULL,
seq_file = NULL,
tax_names = obj$get_data("taxon_names")[[1]],
ranks = obj$get_data("gg_rank")[[1]],
ids = obj$get_data("gg_id")[[1]],
sequences = obj$get_data("gg_seq")[[1]]
)
A taxmap object
(character
of length 1) The file path to save the
taxonomy file.
(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) Sequences
The taxonomy output file has a format like:
228054 k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synech...
844608 k__Bacteria; p__Cyanobacteria; c__Synechococcophycideae; o__Synech...
...
The optional sequence file has a format like:
>1111886
AACGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGAGACCTTCGGGTCTAGTGGCGCACGGGTGCGTA...
>1111885
AGAGTTTGATCCTGGCTCAGAATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGTACGAGAAATCCCGAGC...
...
Other writers:
make_dada2_asv_table()
,
make_dada2_tax_table()
,
write_mothur_taxonomy()
,
write_rdp()
,
write_silva_fasta()
,
write_unite_general()