Make Sintax database

Creates a properly formatted FASTA file for the use as a Sintax database.

Usage

make_sintax_db(taxonomy_table, outfile)

Arguments

taxonomy_table

(Required). A data.frame with sequences and proper information for making a Sintax database, see Details.

outfile

(Required). Name of database file to create (a FASTA file).

Value

No return in R, but a FASTA file (outfile) with properly formatted Header lines is created.

Details

The Sintax algorithm is used by VSEARCH to assign taxonomic information to 16S sequences. It requires a database, which is nothing but a FASTA file of 16S sequences with properly formatted Header-lines.

The taxonomy_table provided as input here must have the columns:

• Header - short unique text for each sequence

• Sequence - the sequences

• Columns domain, phylum, class, order, family, genus, species. Text columns with taxon names.

In some taxonomies the domain rank is named kingdom, but here we use the word domain. You may very well have empty (NA) entries in the taxonomy columns of the table.

References

https://www.biorxiv.org/content/10.1101/074161v1

Examples

if (FALSE) { # \dontrun{
# First, you need a table of the same format as output by vs_sintax:
db.file <- file.path(file.path(path.package("Rsearch"), "extdata"),
                     "sintax_db.fasta")
fasta.file <- file.path(file.path(path.package("Rsearch"), "extdata"),
                        "small.fasta")
tax.tbl <- vs_sintax(fasta_input = fasta.file, database = db.file)

# Inspect tax.tbl to see its columns. You replace the column content with
# your desired taxonomy.
# From such a tax.tbl you create the database file:
make_sintax_db(tax.tbl, outfile = "delete_ma.fasta")
} # }