Summarize a FASTA reference database

Provides an overview of a FASTA reference database: number of sequences, sequence length distribution, and taxonomic coverage at each rank. Supports both prefix-based formats (unite, sintax, greengenes2) and positional formats (dada2, pr2).

Usage

summarize_db(
  file,
  rank_prefixes = c("k__", "p__", "c__", "o__", "f__", "g__", "s__"),
  tax_format = NULL
)

Arguments

file

(Character, required) Path to a FASTA file (plain or gzip).

rank_prefixes

(Character vector) Taxonomic rank prefixes to summarize. Defaults to kingdom through species. Ignored if tax_format is provided.

tax_format

(Character) If provided, one of "unite", "sintax", "greengenes2", or "pr2". Overrides rank_prefixes with the full set from tax_prefixes(). If "auto", the format is detected from the file headers using detect_tax_format(). If NULL (default), rank_prefixes is used as-is.

Value

A list with components:

• n_sequences: total number of sequences

• length_summary: summary statistics of sequence lengths

• ranks: a named integer vector of annotated counts per rank

See also

tax_prefixes(), detect_tax_format(), list_ranks_db()

Author

Adrien Taudière

Examples

db <- system.file("extdata", "example_unite.fasta", package = "dbpq")
summarize_db(db)
#> Database: example_unite.fasta
#> Sequences: 5
#> Sequence length: 68-68 (mean: 68)
#>   k: 5 sequences with annotation
#>   p: 5 sequences with annotation
#>   c: 5 sequences with annotation
#>   o: 5 sequences with annotation
#>   f: 5 sequences with annotation
#>   g: 5 sequences with annotation
#>   s: 5 sequences with annotation
summarize_db(db, tax_format = "unite")
#> Database: example_unite.fasta
#> Sequences: 5
#> Sequence length: 68-68 (mean: 68)
#>   k: 5 sequences with annotation
#>   p: 5 sequences with annotation
#>   c: 5 sequences with annotation
#>   o: 5 sequences with annotation
#>   f: 5 sequences with annotation
#>   g: 5 sequences with annotation
#>   s: 5 sequences with annotation