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