merge_bulk_fastq_python {FLAMES}R Documentation

Merge FASTQ using python. Depreciated

Description

Merges all fastq files in the given folder into a single file.

Usage

merge_bulk_fastq_python(fastq_dir, out_fastq)

Arguments

fastq_dir

Path to the folder containing fastq files to merge

out_fastq

file path to the fastq file which will be created to store all fastq entries. Overwrites existing files

Value

file path to the created merged fastq file 'out_fastq'

Examples

# download the fastq files to merge
temp_path <- tempfile()
bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE)
file_url <-
    "https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data"
# download the required fastq files, and move them to new folder
fastq1 <- bfc[[names(BiocFileCache::bfcadd(bfc, "Fastq1", paste(file_url, "fastq/sample1.fastq.gz", sep = "/")))]]
fastq2 <- bfc[[names(BiocFileCache::bfcadd(bfc, "Fastq2", paste(file_url, "fastq/sample2.fastq.gz", sep = "/")))]]
fastq_dir <- paste(temp_path, "fastq_dir", sep = "/") # the downloaded fastq files need to be in a directory to be merged together
dir.create(fastq_dir)
file.copy(c(fastq1, fastq2), fastq_dir)
unlink(c(fastq1, fastq2)) # the original files can be deleted

# merge the fastq files
out_fastq <- paste0(temp_path, "/outfastq.fastq.gz")
## Not run: 
merge_bulk_fastq(fastq_dir, out_fastq)

## End(Not run)

[Package FLAMES version 1.0.2 Index]