Format taxonomy headers for dada2::addSpecies — format2dada2_species • dbpq

Converts taxonomy headers to the format expected by dada2::addSpecies(): ID Genus Species. Wrapper around format_fasta_db().

Usage

format2dada2_species(
  fasta_db = NULL,
  taxnames = NULL,
  input_format = "auto",
  output_path = NULL
)

Arguments

fasta_db: (Character) Path to a FASTA file. Mutually exclusive with taxnames.
taxnames: (Character vector) Taxonomy header strings (without leading >). Mutually exclusive with fasta_db.
input_format: (Character, default "auto") Input taxonomy format. One of "auto", "sintax", "unite", "greengenes2".
output_path: (Character) If provided and fasta_db is used, write the reformatted FASTA to this path.

Value

If taxnames is used, a character vector. If fasta_db is used, a DNAStringSet with reformatted names.

See also

format_fasta_db(), format2sintax(), format2dada2()

Author

Adrien Taudière

Examples

# UNITE format → dada2_species
format2dada2_species(
  taxnames = "AB123;k__Fungi;g__Aspergillus;s__fumigatus"
)
#> [1] "AB123 Aspergillus fumigatus"

# SINTAX format → dada2_species
format2dada2_species(
  taxnames = "AB123;tax=k:Fungi,g:Aspergillus,s:fumigatus",
  input_format = "sintax"
)
#> [1] "AB123 Aspergillus fumigatus"