mergeFastq: Merge groups of Fastq /Fasta files

In JokingHero/ORFik: Open Reading Frames in Genomics

Merge groups of Fastq /Fasta files

Description

Will use multithreading to speed up process. Only works for Unix OS (Linux and Mac)

Usage

mergeFastq(in_files, out_files, BPPARAM = bpparam())

Arguments

in_files	character specify the full path to the individual fastq.gz files. Seperated by space per file in group: For 2 output files from 4 input files: in_files <- c("file1.fastq file2.fastq". "file3.fastq file4.fastq")
out_files	character specify the path to the FASTQ directory For 2 output files: out_files <- c("/merged/file1&2.fastq", "/merged/file3&4.fastq")
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers

Value

invisible(NULL).

Examples

fastq.folder <- tempdir() # <- Your fastq files
infiles <- dir(fastq.folder, "*.fastq", full.names = TRUE)
## Not run: 
# Seperate files into groups (here it is 4 output files from 12 input files)
in_files <- c(paste0(grep(infiles, pattern = paste0("ribopool-",
               seq(11, 14), collapse = "|"), value = TRUE), collapse = " "),
              paste0(grep(infiles, pattern = paste0("ribopool-",
               seq(18, 19), collapse = "|"), value = TRUE), collapse = " "),
              paste0(grep(infiles, pattern = paste0("C11-",
               seq(11, 14), collapse = "|"), value = TRUE), collapse = " "),
              paste0(grep(infiles, pattern = paste0("C11-",
               seq(18, 19), collapse = "|"), value = TRUE), collapse = " "))

out_files <- paste0(c("SSU_ribopool", "LSU_ribopool", "SSU_WT", "LSU_WT"), ".fastq.gz")
merged.fastq.folder <- file.path(fastq.folder, "merged/")
out_files <- file.path(merged.fastq.folder, out_files)

mergeFastq(in_files, out_files)

## End(Not run)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.