Count sequences in fasta or fastq file

Use grep to count the number of line with only one '+' (fastq, fastq.gz) or lines starting with a '>' (fasta) to count sequences.

Usage

count_seq(file_path = NULL, folder_path = NULL, pattern = NULL)

Arguments

file_path

The path to a fasta, fastq or fastq.gz file

folder_path

The path to a folder with fasta, fastq or fastq.gz files

pattern

A pattern to filter files in a folder. E.g. R2

Value

the number of sequences

Author

Adrien Taudière

Examples

count_seq(file_path = system.file(
  "extdata",
  "ex.fasta",
  package = "MiscMetabar",
  mustWork = TRUE
))
#> [1] 3
count_seq(
  folder_path = system.file("extdata", package = "MiscMetabar"),
  pattern = "*.fasta"
)
#> [1] 100   3   2