Attempts to save taxonomic and sequence information of a taxmap object in the
SILVA FASTA format. If the taxmap object was created using
parse_silva_fasta
, then it should be able to replicate the format
exactly with the default settings.
write_silva_fasta(
obj,
file,
tax_names = obj$get_data("taxon_names")[[1]],
other_names = obj$get_data("other_name")[[1]],
ids = obj$get_data("ncbi_id")[[1]],
start = obj$get_data("start_pos")[[1]],
end = obj$get_data("end_pos")[[1]],
sequences = obj$get_data("silva_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) Alternate names
of taxa. Will be added after the primary name.
(character
named by taxon ids) Sequence ids
(character
) The start position of the
sequence.
(character
) The end position of the
sequence.
(character
named by taxon ids) Sequences
The output file has a format like:
>GCVF01000431.1.2369 Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospiril...
CGUGCACGGUGGAUGCCUUGGCAGCCAGAGGCGAUGAAGGACGUUGUAGCCUGCGAUAAGCUCCGGUUAGGUGGCAAACA
ACCGUUUGACCCGGAGAUCUCCGAAUGGGGCAACCCACCCGUUGUAAGGCGGGUAUCACCGACUGAAUCCAUAGGUCGGU
...
Other writers:
make_dada2_asv_table()
,
make_dada2_tax_table()
,
write_greengenes()
,
write_mothur_taxonomy()
,
write_rdp()
,
write_unite_general()