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_fastaproduces 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
(
logicalof 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