ctk_parseAlignment: Wrapper function for ctk's parseAlignment

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Wrapper function for ctk's parseAlignment

Description

Wrapper function for ctk's parseAlignment

Usage

ctk_parseAlignment(
  filesToRun,
  outFile = paste0(file_path_sans_ext(filesToRun), ".bed"),
  sb = "parseAlignment.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  mutationFile = NULL,
  mapQual = NULL,
  minLen = NULL,
  indelToEnd = 5,
  splitDel = FALSE,
  indelInScore = FALSE,
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_parseAlignment_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_parseAlignment_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 (SAM).
outFile	path to output file (BED).
sb	path to parseAlignment.pl from CTK.
perl	path to PERL.
PATHTOPERLLIB	path to PERL5LIB.
mutationFile	mutation file path, default is NULL.
mapQual	minimum map quality, default is NULL.
minLen	minimum length of read, default is NULL.
indelToEnd	minimum distance from indel to end of read, default is 5.
splitDel	whether to split reads with deletions, TRUE or FALSE (default).
indelInScore	include indels in mutation score count, TRUE or FALSE (default).
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 BED file.

Author(s)

Kathryn Rozen-Gagnon

Examples

testFasta <- system.file("extdata/hg19Small.fa",package="CLIPflexR")
myIndex <-suppressWarnings(bowtie2_index(testFasta, overwrite = TRUE))
testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
FqFile_FF <- ctk_fastqFilter(testFQ,qsFilter="mean:0-29:20",verbose = TRUE)
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)
FqFile_QFColStripped <- ctk_stripBarcode(FqFile_Col,linkerlength=5,inputFormat="fastq")
bam <- suppressWarnings(bowtie_align(FqFile_QFColStripped,myIndex, 
overwrite=TRUE, inputFormat="fastq"))
parsedAlignment <- ctk_parseAlignment(bam)

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