Detect taxonomy format from FASTA headers — detect_tax_format • dbpq

Reads a few sequence headers from a FASTA file and guesses the taxonomy format based on characteristic patterns.

Usage

detect_tax_format(file, n_headers = 20L)

Arguments

file: (Character, required) Path to a FASTA file (plain or gzip).
n_headers: (Integer, default 20) Number of headers to inspect.

Value

A character string: one of "unite", "sintax", "greengenes2", "pr2", or "unknown".

See also

tax_prefixes(), list_ranks_db(), summarize_db()

Examples

db <- system.file("extdata", "example_unite.fasta", package = "dbpq")
detect_tax_format(db)
#> [1] "unite"