Wrapper function for fastx_quality_stats

fastx_quality_stats(
  fileTofqs,
  outFile = file.path(dirname(fileTofqs),
    gsub("\\.fastq|\\.fq|fq\\.gz|fastq\\.gz|\\.fasta|\\.fa|fa\\.gz|fasta\\.gz",
    ".txt", basename(fileTofqs))),
  fqs = "fastx_quality_stats",
  qEncoding = 33,
  stderr = file.path(dirname(fileTofqs), paste0(basename(fileTofqs),
    "_fastx_quality_stats_stderr.txt")),
  stdout = file.path(dirname(fileTofqs), paste0(basename(fileTofqs),
    "_fastx_quality_stats_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 - fasta will only return nucleotide distribution).
outFile: output file name.
fqs: path to fastx_quality_stats from FastX toolkit.
qEncoding: quality encoding, set to either 33 (Sanger Phred+33 encoding/Illumina fastq; default) or NULL (Phred+64 fastq or fasta).
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 unzipped file.

Author

Kathryn Rozen-Gagnon

Examples

testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
FqFile <- decompress(testFQ,overwrite=TRUE)
FqFile_QF <- fastq_quality_filter(FqFile)
Fq_Stats <- fastx_quality_stats(FqFile_QF)