Wrapper function for fastx_clipper

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

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, adapter = "GTGTCAG")