Parses an SILVA FASTA file that can be found at https://www.arb-silva.de/no_cache/download/archive/release_128/Exports/.
parse_silva_fasta(file = NULL, input = NULL, include_seqs = TRUE)
taxmap
The path to a FASTA file containing sequences to use. Either "input" or "file" must be supplied but not both.
(character
) One of the following:
See the example below for what this
looks like. The parser read_fasta
produces output like this.
Each vector should have one base per element.
This is the result of parsers like
read.FASTA
.
This is the result of parsers like
read.fasta
.
Either "input" or "file" must be supplied but not both.
(logical
of length 1) If TRUE
, include
sequences in the output object.
The input file has a format like:
>GCVF01000431.1.2369
Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospiril...
CGUGCACGGUGGAUGCCUUGGCAGCCAGAGGCGAUGAAGGACGUUGUAGCCUGCGAUAAGCUCCGGUUAGGUGGCAAACA
ACCGUUUGACCCGGAGAUCUCCGAAUGGGGCAACCCACCCGUUGUAAGGCGGGUAUCACCGACUGAAUCCAUAGGUCGGU
...
Other parsers:
extract_tax_data()
,
lookup_tax_data()
,
parse_dada2()
,
parse_edge_list()
,
parse_greengenes()
,
parse_mothur_tax_summary()
,
parse_mothur_taxonomy()
,
parse_newick()
,
parse_phylo()
,
parse_phyloseq()
,
parse_qiime_biom()
,
parse_rdp()
,
parse_tax_data()
,
parse_ubiome()
,
parse_unite_general()