Format taxonomy headers to SINTAX format

Converts taxonomy headers to the VSEARCH SINTAX format (>ID;tax=k:Kingdom,p:Phylum,...). Wrapper around format_fasta_db().

Usage

format2sintax(
  fasta_db = NULL,
  taxnames = NULL,
  input_format = "auto",
  output_path = NULL,
  id_prefix = "seq"
)

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", "unite", "greengenes2", "dada2".

output_path

(Character) If provided and fasta_db is used, write the reformatted FASTA to this path.

id_prefix

(Character, default "seq") Prefix for synthetic sequence IDs generated when the input has none (e.g. "dada2").

Value

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

See also

format_fasta_db(), format2dada2(), format2dada2_species()

Author

Adrien Taudière

Examples

# UNITE format → SINTAX
format2sintax(taxnames = "AB123;k__Fungi;p__Ascomycota;c__Sordariomycetes")
#> [1] "AB123;tax=k:Fungi,p:Ascomycota,c:Sordariomycetes"

# Greengenes2 format → SINTAX
format2sintax(
  taxnames = "abc123 d__Bacteria;p__Pseudomonadota",
  input_format = "greengenes2"
)
#> [1] "abc123;tax=d:Bacteria,p:Pseudomonadota"

# dada2 trainset (taxonomy-only, positional) → SINTAX with synthetic IDs
format2sintax(
  taxnames = "Bacteria;Pseudomonadota;Gammaproteobacteria;Vibrio;",
  input_format = "dada2",
  id_prefix = "SILVA_"
)
#> [1] "SILVA_000001;tax=d:Bacteria,p:Pseudomonadota,c:Gammaproteobacteria,o:Vibrio"