Wrapper function for galaxy's joinWrapper

ctk_joinWrapper(
  file1,
  file2,
  field1,
  field2,
  mode,
  outFile = file.path(dirname(file1), paste0("Unique_", basename(file1))),
  sb = "joinWrapper.py",
  python = "python",
  stderr = file.path(dirname(file1), paste0(basename(file1),
    "_ctk_joinWrapper_stderr.txt")),
  stdout = file.path(dirname(file1), paste0(basename(file1),
    "_ctk_joinWrapper_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE,
  writelog = T
)

Arguments

file1: path to file 1 to join (BED or tab delimited text).
file2: path to file 2 to join (BED or tab delimited text).
field1: field/column for file 1 join.
field2: field/column for file 2 join.
mode: join mode.
outFile: path to output file.
sb: path to joinWrapper.py from Galaxy
python: path to python.
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 joined file.

Author

Kathryn Rozen-Gagnon

Examples

if (FALSE) {
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"))
mutationFile <- system.file("extdata/Fox3_Std_small_mutation.txt",package="CLIPflexR")
parsedAlignment <- ctk_parseAlignment(bam,mutationFile=mutationFile)
uniqueTags <- ctk_tag2collapse(parsedAlignment,weight=FALSE,randomBarcode=FALSE,
weightInName=FALSE,verbose=TRUE)
ctk_joinWrapper(mutationFile,uniqueTags,4,4,"N",verbose=TRUE)
}