ctk_joinWrapper: Wrapper function for galaxy's joinWrapper

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Wrapper function for galaxy's joinWrapper

Description

Wrapper function for galaxy's joinWrapper

Usage

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(s)

Kathryn Rozen-Gagnon

Examples

## Not run: 
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)

## End(Not run)

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