Wrapper function for fastx_collapser

fastx_collapser(
  fileTofxc,
  outFile = file.path(dirname(fileTofxc), gsub("\\.fastq|\\.fq|\\.fa|\\.fasta",
    "_collapse.fasta", basename(fileTofxc))),
  fxc = "fastx_collapser",
  qEncoding = NULL,
  stderr = file.path(dirname(fileTofxc), paste0(basename(fileTofxc),
    "_fastx_collapse_stderr.txt")),
  stdout = file.path(dirname(fileTofxc), paste0(basename(fileTofxc),
    "_fastx_collapse_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE,
  writelog = T
)

Arguments

fileTofxc: path to file to process (fastq or fasta).
outFile: output file name (will be formatted as a fasta).
fxc: path to fastx_collapser 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).
writelog: write stderr/stdout logs, TRUE (default) or FALSE.

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)
FqFile_QFCollapsed <- fastx_collapser(FqFile_QF)