parse_silva_fasta: Parse SILVA FASTA release

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Parse SILVA FASTA release

Description

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) If TRUE, include sequences in the output object.

Details

The input file has a format like:

 >GCVF01000431.1.2369
Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospiril...
CGUGCACGGUGGAUGCCUUGGCAGCCAGAGGCGAUGAAGGACGUUGUAGCCUGCGAUAAGCUCCGGUUAGGUGGCAAACA
ACCGUUUGACCCGGAGAUCUCCGAAUGGGGCAACCCACCCGUUGUAAGGCGGGUAUCACCGACUGAAUCCAUAGGUCGGU
... 

Value

taxmap

See Also

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()

metacoder documentation built on April 3, 2025, 8:39 p.m.