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Combine FASTA/FASTQ files in a directory into a single file or object

Source: R/fastx_combine_files.R
fastx_combine_files.Rd

fastx_combine_files combines all FASTA or FASTQ files within a specified directory into a single output file or a tibble object.

Usage

fastx_combine_files(
  files_dir,
  output_file = NULL,
  file_ext = ".fq",
  file_format = "fastq",
  tmpdir = NULL
)

Arguments

files_dir

(Required). A character string specifying the path to the directory containing the files to be combined. Files must be uncompressed.

output_file

(Optional). A character string specifying the name of the output file. If NULL (default), the combined data is returned as a FASTA/FASTQ object depending on file_format instead of being written to a file.

file_ext

(Optional). File extension of the files to be combined. Defaults to ".fq".

file_format

(Optional). Format of files to be combined and the desired output format: either "fasta" or "fastq" (default). See Details.

tmpdir

(Optional). Path to the directory where temporary files should be written when tables are used as input or output. Defaults to NULL, which resolves to the session-specific temporary directory (tempdir()).

Value

A tibble or NULL.

If output_file is specified, the combined sequences are written to the specified file.

If output_file is NULL, the combined sequences are returned as a tibble in the format specified by file_format.

Details

files_dir must contain uncompressed FASTA or FASTQ files matching the specified file_ext.

All files with the specified file_ext in files_dir are concatenated into a single output file or tibble.

A FASTA object is a tibble containing the columns Header and Sequence. A FASTQ object is a tibble containing the columns Header, Sequence, and Quality.

If output_file is specified, the combined sequences are written to this file in the format specified by file_format.

If output_file is NULL, the combined sequences are returned as a tibble in the format specified by file_format, and no file is written.

Examples

# Define arguments
files_dir <- system.file("extdata", package = "Rsearch")
output_file <- NULL
file_ext <- ".fq"
file_format <- "fastq"

# Combine files and return tibble object
combined_files <- fastx_combine_files(files_dir = files_dir,
                                      output_file = output_file,
                                      file_ext = file_ext,
                                      file_format = file_format)

# Combine files and write to output file

# Define output file name
out <- tempfile(fileext = ".fastq")

fastx_combine_files(files_dir = files_dir,
                    output_file = out,
                    file_ext = file_ext,
                    file_format = file_format)