Count lines matching a pattern in a FASTA file

Count lines (sequences if fasta file) matching a pattern. Accepts gzip files. May not work on Windows.

Usage

count_pattern_db(file, pattern = ">")

Arguments

file

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

pattern

(Character, default ">") A pattern to search for.

Value

An integer, the number of matching lines.

See also

filter_db(), count_seq_db()

Author

Adrien Taudière

Examples

db <- system.file("extdata", "example_unite.fasta", package = "dbpq")
count_pattern_db(db, "Amanita")
#> [1] 2