parse_unite_general: Parse UNITE general release FASTA

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

Parse UNITE general release FASTA

Description

Parse the UNITE general release FASTA file

Usage

parse_unite_general(input = NULL, file = NULL, include_seqs = TRUE)

Arguments

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.
file	The path to a FASTA file containing sequences to use. 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:

>Glomeromycota_sp|KJ484724|SH523877.07FU|reps|k__Fungi;p__Glomeromycota;c__unid...
ATAATTTGCCGAACCTAGCGTTAGCGCGAGGTTCTGCGATCAACACTTATATTTAAAACCCAACTCTTAAATTTTGTAT...

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_phyloseq(), parse_phylo(), parse_qiime_biom(), parse_rdp(), parse_silva_fasta(), parse_tax_data(), parse_ubiome()

metacoder documentation built on April 4, 2023, 9:08 a.m.