parse_unite_general {metacoder}

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_phylo(), parse_phyloseq(), parse_qiime_biom(), parse_rdp(), parse_silva_fasta(), parse_tax_data(), parse_ubiome()