ctk_fastqFilter: Wrapper function for ctk's fastq_filter

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Wrapper function for ctk's fastq_filter

Description

Wrapper function for ctk's fastq_filter

Usage

ctk_fastqFilter(
  filesToRun,
  outFile = file.path(dirname(fileToRun), paste("FF_", basename(fileToRun), sep = "")),
  sb = "fastq_filter.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  fastqFormat = "sanger",
  indexPosition = NULL,
  qsFilter = NULL,
  maxN = NULL,
  outputFormat = "fastq",
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_fastqFilter_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_fastqFilter_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).
outFile	output file (fastq).
sb	path to fastq_filter.pl from CTK.
perl	path to PERL.
PATHTOPERLLIB	path to PERL5LIB.
fastqFormat	fastq format used, can be "sanger" (default) or "solexa".
indexPosition	position and sequence of index in read, default is NULL; set "position:seqeunce" to specify (e.g. "1:CATCGC").
qsFilter	set quality score filter, default is NULL; set method:start-end:score to specify (e.g. "mean:0-29:20"; starts/ends are 0-based).
maxN	maximum number of unknown nucleotides (N) allowed, default is NULL; set to integer to specify.
outputFormat	output format, "fastq" (default) or "fasta".
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 filtered file in specified format.

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)

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