parse_unite_general: Parse UNITE general release FASTA

Description Usage Arguments Details Value See Also

View source: R/parsers.R

Description

Parse the UNITE general release FASTA file

Usage

1
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:

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2
>Glomeromycota_sp|KJ484724|SH523877.07FU|reps|k__Fungi;p__Glomeromycota;c__unid...
ATAATTTGCCGAACCTAGCGTTAGCGCGAGGTTCTGCGATCAACACTTATATTTAAAACCCAACTCTTAAATTTTGTAT...

Value

taxmap

See Also

Other parsers: 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_ubiome


grunwaldlab/metacoder documentation built on Oct. 2, 2018, 10:25 p.m.