Reformat Taxonomic Lineage using taxonkit reformat2

Reformat lineage in chosen ranks, allowing more ranks than 'reformat'. This function only accepts TaxIDs as input (not lineage strings).

taxonkit_reformat2(
  file_path,
  format_string = "",
  miss_rank_repl = "",
  miss_taxid_repl = "",
  no_ranks = c("no rank", "clade"),
  show_lineage_taxids = FALSE,
  taxid_field = 1,
  trim = FALSE,
  text = FALSE,
  data_dir = NULL
)

Arguments

file_path

The path to the input file with taxonomic IDs. Or file text (text=TRUE)

format_string

The output format string with placeholders for each rank. Use "|" to set multiple ranks, the first valid one will be output. Example: "domain|acellular root|superkingdom;phylum;class;order;family;genus;species"

miss_rank_repl

The replacement string for missing rank.

miss_taxid_repl

The replacement string for missing taxid.

no_ranks

A character vector of rank names considered as "no-rank". A lineage might have many "no rank" ranks, we only keep the last one below known ranks. Default: c("no rank", "clade")

show_lineage_taxids

Logical, indicating whether to show corresponding taxids of reformatted lineage (default: FALSE)

taxid_field

The field index of taxid. Input data should be tab-separated (default: 1)

trim

Logical, indicating whether to not replace missing ranks lower than the rank of the current node (default: FALSE)

text

logical. If TRUE, file_path is treated as text input

data_dir

directory containing nodes.dmp and names.dmp (default "/Users/asa/.taxonkit")

Value

A character vector containing the reformatted taxonomic lineages.

Details

Key differences from taxonkit_reformat():

• Input: only accepts TaxIDs

• Format: accepts more rank placeholders, not just the seven canonical ones

• Format: uses full rank names like "species" rather than "s"

• Format: supports multiple ranks in one placeholder like "subspecies|strain"

• No automatic prefix addition (but you can add them in the format string)

See also

Other Rtaxonkit: check_taxonkit(), download_taxonkit_dataset(), install_taxonkit(), name_or_id2df(), taxonkit_filter(), taxonkit_lca(), taxonkit_lineage(), taxonkit_list(), taxonkit_name2taxid(), taxonkit_reformat()

Examples

if (FALSE) { # \dontrun{
# Example 1: Basic usage with default format
taxids <- c("9606", "376619", "11932")
tmp_file <- tempfile()
writeLines(taxids, tmp_file)
result <- taxonkit_reformat2(tmp_file)

# Example 2: Custom format with multiple rank options
result2 <- taxonkit_reformat2(
  tmp_file,
  format_string = "{domain|acellular root|superkingdom};{kingdom};{phylum};{class}"
)

# Example 3: With text input
taxonkit_reformat2(
  "2759\n2\n10239",
  format_string = "{domain|acellular root|superkingdom}",
  text = TRUE
)
# Clean up
unlink(tmp_file)
} # }