Wrapper function for ctk's stripBarcode

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

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)
#> fastq_filter.pl command is /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq_filter.pl
#> fastq_filter.pl arguments are /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq_filter.pl  -if sanger  -of fastq  -f mean:0-29:20  /Users/runner/work/_temp/Library/CLIPflexR/extdata/Fox3_Std_small.fq.gz  /Users/runner/work/_temp/Library/CLIPflexR/extdata/FF_Fox3_Std_small.fq.gz 
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)
#> fastq_filter.pl command is /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq2collapse.pl
#> fastq_filter.pl arguments are /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq2collapse.pl  /Users/runner/work/_temp/Library/CLIPflexR/extdata/QT_FF_Fox3_Std_small_clip.fq  /Users/runner/work/_temp/Library/CLIPflexR/extdata/Collapsed_QT_FF_Fox3_Std_small_clip.fq 
FqFile_QFColStripped <- ctk_stripBarcode(FqFile_Col,linkerlength=5,inputFormat="fastq")