pr2_export: Export the PR2 database (one file)

In vaulot/dvutils: A set of utilities

Description

This will save the pr2 database in variety of format. The files are compressed as .gz

• "fasta" - the description line is taylored for different applications (usearch, mothur, dada2, blast). for the application dada2 2 kinds of files can be produced one for otu assignement and one for species

• "taxo" - the file is saved with the mothur format

• "metadata" - only the metadata

• "merged" - the whole database in a single file

Notes

• The data are NOT filtered in any way, this should be done before saving

• The following fields are needed to create the sequence labels :

  • pr2_sample_type, gb_strain, gb_clone, gb_specimen_voucher

  • gene, organelle

Usage

pr2_export(
  pr2_select,
  file_name,
  file_type = "fasta",
  file_format = "fasta_taxo_long",
  taxo_levels_number = 9
)

Arguments

pr2_select	data frame - the pr2 database or an extract of the pr2 database
file_name	character - full path of file where to save
file_type	character - one of "fasta", "taxo", "metadata", "merged", "merged_excel"
file_format	character - one of "UTAX", "fasta_taxo_short","fasta_taxo_long","dada2", "dada2_species","mothur"

Value

Write the files in compressed format (.gz)

Examples

pr2_export(pr2, "C:/Daniel/myfile.fas", "fasta", "mothur", 9)

vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.