clean_DNA_file {baseq}

Clean DNA file

Description

This function reads a multi FASTA file containing DNA sequences, removes any characters other than A, T, G, and C, and writes the cleaned sequences to a new multi FASTA file. The output file name is generated from the input file name with the suffix '_clean.fasta'.

Usage

clean_DNA_file(input_file, output_dir = "")

Arguments

input_file

The name of the input multi FASTA file.

output_dir

The directory where the output file will be saved. If not given, the output file will be saved in the same directory as the input file.

Value

A character string specifying the path to the output FASTA file.

Examples

#sample_file_path_three <- system.file("extdata", "sample2_fa.fasta", package = "baseq")
#tempdir <- tempdir()
#temp_file_path <- file.path(tempdir, basename(sample_file_path_three))
#file.copy(sample_file_path_three, temp_file_path, overwrite = TRUE)
#clean_DNA_file(temp_file_path, output_dir = tempdir)

# Write to working directory
# clean_DNA_file(file_path)

# Write to custom directory
# clean_DNA_file(file_path, output_dir = "/path/to/directory/")