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Format a fasta database in dada2 format

Source: R/taxonomy.R
format2dada2.Rd

lifecycle-experimental

First format in sintax format and then in dada2 format

Usage

format2dada2(
  fasta_db = NULL,
  taxnames = NULL,
  output_path = NULL,
  from_sintax = TRUE,
  pattern_to_remove = NULL,
  ...
)

Arguments

fasta_db

A link to a fasta files

taxnames

A list of names to format. You must specify either fasta_db OR taxnames, not both.

output_path

(optional) A path to an output fasta files. Only used if fasta_db is set.

from_sintax

(logical, default FALSE) Is the original fasta file in sintax format?

pattern_to_remove

(a regular expression) Define a pattern to remove. For example, pattern_to_remove = "\|rep.*" remove all character after '|rep' to force dada2::assignTaxonomy() to not use the database as a Unite-formated database

...

Additional arguments passed on to format2sintax() function

Value

Either an object of class DNAStringSet or a vector of reformated names

See also

format2dada2_species(), format2sintax()

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
f <- system.file("extdata", "mini_UNITE_fungi.fasta.gz",
  package = "MiscMetabar"
)
format2dada2(fasta_db = f, from_sintax = FALSE)
} # }