ctk_stripBarcode: Wrapper function for ctk's stripBarcode

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Wrapper function for ctk's stripBarcode

Description

Wrapper function for ctk's stripBarcode

Usage

ctk_stripBarcode(
  filesToRun,
  outFile = paste(file_path_sans_ext(fileToRun), "_rm5.", file_ext(fileToRun), sep = ""),
  sb = "stripBarcode.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  linkerlength = 27,
  inputFormat = "fasta",
  barcodeStartWith = NULL,
  barcodeEndWith = NULL,
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_stripBarcode_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_stripBarcode_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE,
  writelog = T
)

Arguments

filesToRun	path to file to process (fastq or fasta).
outFile	path to output file (fastq or fasta).
sb	path to stripBarcode.pl from CTK.
perl	path to PERL.
PATHTOPERLLIB	path to PERL5LIB.
linkerlength	length of barcode/linker sequences (default is 27).
inputFormat	input file format, "fasta" (default) or "fastq"
barcodeStartWith	filter sequences based on the starting nucleotides in the barcode.
barcodeEndWith	filter sequences based on the ending nucleotides in the barcode.
stderr	path to stdout 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, TRUE or FALSE (default).
writelog	write stderr/stdout logs, TRUE (default) or FALSE.

Value

path to file with index stripped, in the same format as the input 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)
FqFile_QF <- fastq_quality_trimmer(FqFile_clipped)
FqFile_Col <- ctk_fastq2collapse(FqFile_QF,verbose=TRUE)
FqFile_QFColStripped <- ctk_stripBarcode(FqFile_Col,linkerlength=5,inputFormat="fastq")

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