Convert FASTQ file(s) to FASTA file(s)

Convert one or several FASTQ files (optionally gzip-compressed) to FASTA format. For each input file, the @ sign starting a FASTQ sequence header is replaced by the > sign required by the FASTA format, and the quality lines are dropped. Output files keep the input base name with the extension changed to .fasta.

Inspired by https://github.com/ambuvjyn/baseq.

Usage

fastq_to_fasta(fastq_files, output_folder = tempdir(), force = FALSE)

Arguments

fastq_files

(character, required) One or more paths to FASTQ files. The .fastq, .fq, .fastq.gz and .fq.gz extensions are recognized (case-insensitive).

output_folder

(character, default: tempdir()) Folder where the FASTA files are written. Created if it does not exist.

force

(logical, default: FALSE) If FALSE, existing output files are not overwritten and an error is thrown instead.

Value

A character vector of the paths to the output FASTA files (invisibly named by the input files).

Author

Adrien Taudière

Examples

# \donttest{
fq <- system.file("extdata", "ex.fastq", package = "MiscMetabar")
out <- fastq_to_fasta(fq, output_folder = tempdir())
#> ✔ Wrote 1 FASTA file to /tmp/RtmpMeUGPY.
readLines(out, n = 2)
#> [1] ">M03493:483:000000000-KW735:1:1101:10710:1281 1:N:0:17"                                                                                                                                                                                                                                                       
#> [2] "CTTGTTGGAGGGCAAGTCTGGTGCCCGCAGCCGCGGTAATTCCAGCTCCAATAGCGNNTNNTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAATTTCGGGATNNATGGGTTGGTCACGCCCTCGGTATGTACTGATTGCATTGGTGCTCACCTTCTAAGGAACCATGATGTCATTCGTTTGATGTGGTTGGGAATGAGGACTGTTATCTTGAAAAAATTGGAGGGTTTAAAGCAGTCTAACGCTTTAATACATTATCATGGAATAATGAAATCGGACAGCCGATTATATTTTGTTGGCG"
# }