write_unite_general: Write an imitation of the UNITE general FASTA database

Description Usage Arguments Details See Also

View source: R/writers.R

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

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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:

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

See Also

Other writers: write_greengenes, write_mothur_taxonomy, write_rdp


grunwaldlab/metacoder documentation built on Nov. 30, 2018, 7:53 p.m.