write_unite_general: Write an imitation of the UNITE general FASTA database

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Write an imitation of the UNITE general FASTA database

Description

Attempts to save taxonomic and sequence information of a taxmap object in the UNITE general FASTA format. If the taxmap object was created using parse_unite_general, then it should be able to replicate the format exactly with the default settings.

Usage

write_unite_general(
  obj,
  file,
  tax_names = obj$get_data("taxon_names")[[1]],
  ranks = obj$get_data("unite_rank")[[1]],
  sequences = obj$get_data("unite_seq")[[1]],
  seq_name = obj$get_data("organism")[[1]],
  ids = obj$get_data("unite_id")[[1]],
  gb_acc = obj$get_data("acc_num")[[1]],
  type = obj$get_data("unite_type")[[1]]
)

Arguments

obj	A taxmap object
file	(character of length 1) The file path to save the sequence fasta file. This is optional.
tax_names	(character named by taxon ids) The names of taxa
ranks	(character named by taxon ids) The ranks of taxa
sequences	(character named by taxon ids) Sequences
seq_name	(character named by taxon ids) Name of sequences. Usually a taxon name.
ids	(character named by taxon ids) UNITE sequence ids
gb_acc	(character named by taxon ids) Genbank accession numbers
type	(character named by taxon ids) What type of sequence it is. Usually "rep" or "ref".

Details

The output file has a format like:

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

See Also

Other writers: make_dada2_asv_table(), make_dada2_tax_table(), write_greengenes(), write_mothur_taxonomy(), write_rdp(), write_silva_fasta()

metacoder documentation built on April 4, 2023, 9:08 a.m.