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Filter a FASTA database by taxonomic pattern

Source: R/modify.R
filter_db.Rd

lifecycle-experimental

Filters sequences from a FASTA database whose header lines match a given pattern. Accepts gzip files. May not work on Windows.

Usage

filter_db(
  ref_fasta,
  pattern,
  output = NULL,
  force_two_lines_per_seq = TRUE,
  keep_temporary_files = FALSE
)

Arguments

ref_fasta

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

pattern

(Character, required) A pattern to search for in sequence headers.

output

(Character, required) Path to the output FASTA file (must not be gzipped).

force_two_lines_per_seq

(Logical, default TRUE) Force the FASTA file to have exactly two lines per sequence (one header, one nucleotide line). If FALSE, the input must already be in this format.

keep_temporary_files

(Logical, default FALSE) If TRUE and force_two_lines_per_seq is TRUE, keep intermediate temporary files.

Value

The path to the output file (invisibly).

See also

count_pattern_db()

Author

Adrien Taudière

Examples

db <- system.file("extdata", "example_unite.fasta", package = "dbpq")
out <- tempfile(fileext = ".fasta")
filter_db(db, "Amanita", output = out)
count_seq_db(out)
#> [1] 2