fastx_clipper: Wrapper function for fastx_clipper

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Wrapper function for fastx_clipper

Description

Wrapper function for fastx_clipper

Usage

fastx_clipper(
  fileTofqs,
  outFile = paste0(file_path_sans_ext(fileTofqs), "_clip.", file_ext(fileTofqs)),
  fqc = "fastx_clipper",
  length = 18,
  adapter = "GTGTCAGTCACTTCCAGCGG",
  qEncoding = NULL,
  writelog = T,
  stderr = file.path(dirname(fileTofqs), paste0(basename(fileTofqs),
    "_fastx_clipper_stderr.txt")),
  stdout = file.path(dirname(fileTofqs), paste0(basename(fileTofqs),
    "_fastx_clipper_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE
)

Arguments

fileTofqs	path to file to process (fastq or fasta).
outFile	output file path.
fqc	path to fastx_clipper from FastX toolkit.
length	minimum sequence length, default is 18 (set to integer).
adapter	adapter to remove (default is "GTGTCAGTCACTTCCAGCGG", specify a string to change adapter sequence).
qEncoding	quality encoding, set to either 33 (Sanger Phred+33 encoding/Illumina fastq) or NULL (Phred+64 fastq or fasta; default).
writelog	write stderr/stdout logs, TRUE (default) or FALSE.
stderr	path to stderr file.
stdout	path to stdout file.
useClipRConda	use conda environment installed by Herper, TRUE (default) or FALSE.
additional_Args	additional arguments to be passed to system call.
verbose	print messages to screen, TRUE or FALSE (default).

Value

path to clipped file

Author(s)

Kathryn Rozen-Gagnon

Examples

testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
FqFile_FF <- ctk_fastqFilter(testFQ,qsFilter = "mean:0-29:20",verbose=TRUE)
FqFile <- decompress(FqFile_FF,overwrite=TRUE)
FqFile_clipped <- fastx_clipper(FqFile,length=20, adapter = "GTGTCAG")

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.