TestMIXCR.R
In elmerfer/RMiXCR: An easy wrapper for MiXCR software
# ##check on consolo the java version
# java.version <- system2(command = "java", args = "--version", stdout = TRUE)
# java.version <- unlist(stringr::str_split(java.version," "))[2]
#
# mixcr.path <- "/media/respaldo4t/mixcr3/mixcr.jar"
# system2(command= "java",
# args = c(paste0("-Xmx4g"),
# paste0("-Xms3g"),
# paste0("-jar ",mixcr.path),"analyze","--help"))
#
# out <- system2(command= "java",
# args = c(paste0("-Xmx4g"),
# paste0("-Xms3g"),
# paste0("-jar ",mixcr.path),
# # "-v",
# "analyze",
# "shotgun",
# "--species mmu",
# "--starting-material rna",
# "--only-productive",
# "/media/respaldo4t/Consultorias/Montes/mouse/D120T33.R1.fastq.gz",
# "/media/respaldo4t/Consultorias/Montes/mouse/D120T33.R2.fastq.gz",
# "analysis",
# "--export "
# #
#
# ),
# stdout = TRUE
# )
#
# destdir <- "/media/respaldo4t/Consultorias/Montes/mouse/"
# sample <- "D120T33"
# analysis.files <- list.files(getwd(),full.names = TRUE)
# analysis.files <- analysis.files[stringr::str_detect(analysis.files,"analysis.")]
# destination.files <- file.path(destdir, paste0(sample,"_",basename(analysis.files)))
# file.copy(analysis.files,file.path(destdir, paste0(sample,"_",basename(analysis.files))))
# file.remove(analysis.files)
#
#
# system2(command= "java",
# args = c(paste0("-Xmx4g"),
# paste0("-Xms3g"),
# paste0("-jar ",mixcr.path), "analyze","help" ))
#
# targets <- openxlsx::read.xlsx("/media/respaldo4t/Consultorias/Montes/mouse/TablaURLS.xlsx")
# log.file <- "/media/respaldo4t/Consultorias/Montes/mouse/TablaURLS.xlsx"
# lapply(1:nrow(targets), function(id){
# fileID1 <- rev(unlist(stringr::str_split(targets$url1[id],"/")))[2]
# fileID2 <- rev(unlist(stringr::str_split(targets$url2[id],"/")))[2]
# fileOUT <- targets$Name[id]
# cat(paste0("\n-----------------" ))
# cat(paste0("\n",fileID1, ": R1" ))
# arg2 <- paste0("wget --load-cookies /tmp/cookies.txt \"https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=FILEID' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\\1\\n/p'",")","&id=FILEID\"")
# arg2 <- stringr::str_replace_all(arg2, "FILEID",fileID1)
# arg2 <- paste(arg2," -O ",paste0("/media/respaldo4t/Consultorias/Montes/mouse/","D120T",fileOUT,".R1.fastq.gz")," && rm -rf /tmp/cookies.txt")
# system(command = arg2, ignore.stdout = TRUE)
# cat(paste0("\n",fileID1, ": R2" ))
#
# arg2 <- paste0("wget --load-cookies /tmp/cookies.txt \"https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=FILEID' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\\1\\n/p'",")","&id=FILEID\"")
# arg2 <- stringr::str_replace_all(arg2, "FILEID",fileID2)
# arg2 <- paste(arg2," -O ",paste0("/media/respaldo4t/Consultorias/Montes/mouse/","D120T",fileOUT,".R2.fastq.gz")," && rm -rf /tmp/cookies.txt")
# system(command = arg2, ignore.stdout = TRUE)
#
# })
mixcr.path <- "/media/respaldo4t/mixcr3/mixcr.jar"
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar align --species hsa --chains TCR --parameters rna-seq -OallowPartialAlignments=true --threads 8 ${INPUT_FASTQ}.R1.fastq.gz ${INPUT_FASTQ}.R2.fastq.gz ${OUTPUT_FILE}.alignments.vdjca
species <- "mmu"#hsa for human
nThreads <- 6
file1 <- "/media/respaldo4t/Consultorias/Montes/mouse/D120T33.R1.fastq.gz"
file2 <- stringr::str_replace(file1,".R1.fasta",".R2.fasta")
align.ofile <- file.path(dirname(file1), paste0(basename(file1),".alignments.vdjca"))
base.args <- c(paste0("-Xmx4g"),paste0("-Xms3g"),paste0("-jar ",mixcr.path))
RunMiXCR <- function(sbj, species = c("hsa","mmu"), nTreads){
software <- RMiXCR:::.OpenConfigFile()
cat(paste0("\nAlignment"))
if(missing(nTreads)){
nt <- parallel::detectCores()
nTreads <- ifelse(nt-2 < 1, 1, nt)
message(paste0("\nRunning with ", nt, " Cores"))
}
species <- match.arg(species, c("hsa","mmu") )
file1 <- sbj
file2 <- stringr::str_replace(file1,".R1.fasta",".R2.fasta")
align.ofile <- file.path(dirname(file1), paste0(basename(file1),".alignments.vdjca"))
system2(command= "java",
args = c(software$mixcr$base.args,"align",
paste0("--species ",species),
"--chains TCR",
"--parameters rna-seq",
"-OallowPartialAlignments=true",
paste0("--threads ",nThreads),
file1,
file2,
align.ofile))
if(file.exists(align.ofile)==FALSE){
stop(align.ofile)
}
assemble.ofile <- file.path(dirname(file1), paste0(basename(file1),".clones.clns"))
cat(paste0("\nAssembling"))
system2(command = "java",
args = c(software$mixcr$base.args,
"assemble",
paste0("--threads ",nThreads),
"-OmaxBadPointsPercent=0",
align.ofile,
assemble.ofile
))
if(file.exists(assemble.ofile)==FALSE){
stop(assemble.ofile)
}
cat(paste0("\nExporting clones to Excel file"))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "--chains TCR",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR -p min ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.vmin.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "--chains TCR",
"-p min",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns","vmin.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.vdetails.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "-count",
"-vhit", "-dhit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".vdetails.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRA -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRA.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRA", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRA.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRB -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRB.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRB", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRB.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRG -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRG.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRG", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRG.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRD -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRD.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRD", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRD.clones.tab")
))
to.excel <- lapply(c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab"), function(x){
if(file.exists(stringr::str_replace(assemble.ofile,".clns",x))){
return(read.table(stringr::str_replace(assemble.ofile,".clns",x),h=T, sep="\t"))
}else{
return(NA)
}
})
aux.files.subfix <- c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab")
names(to.excel) <- stringr::str_remove(c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab"),".tab")
openxlsx::write.xlsx(to.excel, stringr::str_replace(assemble.ofile,".clns",".xlsx"))
file.remove(stringr::str_replace(assemble.ofile,".clns",aux.files.subfix))
return(invisible(aux.files.subfix))
}
cat(paste0("\nAlignment"))
system2(command= "java",
args = c(base.args,"align",
paste0("--species ",species),
"--chains TCR",
"--parameters rna-seq",
"-OallowPartialAlignments=true",
paste0("--threads ",nThreads),
file1,
file2,
align.ofile))
if(file.exists(align.ofile)==FALSE){
stop(align.ofile)
}
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar assemble --threads 8 -OmaxBadPointsPercent=0 ${OUTPUT_FILE}.alignments.vdjca ${OUTPUT_FILE}.clones.clns
assemble.ofile <- file.path(dirname(file1), paste0(basename(file1),".clones.clns"))
cat(paste0("\nAssembling"))
system2(command = "java",
args = c(base.args,
"assemble",
paste0("--threads ",nThreads),
"-OmaxBadPointsPercent=0",
align.ofile,
assemble.ofile
))
if(file.exists(assemble.ofile)==FALSE){
stop(assemble.ofile)
}
#Exporting clones to tab-delimited file
cat(paste0("\nExporting clones to tab-delimited file"))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "--chains TCR",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR -p min ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.vmin.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "--chains TCR",
"-p min",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns","vmin.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.vdetails.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "-count",
"-vhit", "-dhit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".vdetails.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRA -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRA.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRA", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRA.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRB -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRB.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRB", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRB.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRG -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRG.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRG", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRG.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRD -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRD.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRD", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRD.clones.tab")
))
to.excel <- lapply(c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab"), function(x){
if(file.exists(stringr::str_replace(assemble.ofile,".clns",x))){
return(read.table(stringr::str_replace(assemble.ofile,".clns",x),h=T, sep="\t"))
}else{
return(NA)
}
})
aux.files.subfix <- c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab")
names(to.excel) <- stringr::str_remove(c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab"),".tab")
openxlsx::write.xlsx(to.excel, stringr::str_replace(assemble.ofile,".clns",".xlsx"))
file.remove(stringr::str_replace(assemble.ofile,".clns",aux.files.subfix))
elmerfer/RMiXCR documentation built on May 27, 2023, 5:08 a.m.
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# ##check on consolo the java version
# java.version <- system2(command = "java", args = "--version", stdout = TRUE)
# java.version <- unlist(stringr::str_split(java.version," "))[2]
#
# mixcr.path <- "/media/respaldo4t/mixcr3/mixcr.jar"
# system2(command= "java",
# args = c(paste0("-Xmx4g"),
# paste0("-Xms3g"),
# paste0("-jar ",mixcr.path),"analyze","--help"))
#
# out <- system2(command= "java",
# args = c(paste0("-Xmx4g"),
# paste0("-Xms3g"),
# paste0("-jar ",mixcr.path),
# # "-v",
# "analyze",
# "shotgun",
# "--species mmu",
# "--starting-material rna",
# "--only-productive",
# "/media/respaldo4t/Consultorias/Montes/mouse/D120T33.R1.fastq.gz",
# "/media/respaldo4t/Consultorias/Montes/mouse/D120T33.R2.fastq.gz",
# "analysis",
# "--export "
# #
#
# ),
# stdout = TRUE
# )
#
# destdir <- "/media/respaldo4t/Consultorias/Montes/mouse/"
# sample <- "D120T33"
# analysis.files <- list.files(getwd(),full.names = TRUE)
# analysis.files <- analysis.files[stringr::str_detect(analysis.files,"analysis.")]
# destination.files <- file.path(destdir, paste0(sample,"_",basename(analysis.files)))
# file.copy(analysis.files,file.path(destdir, paste0(sample,"_",basename(analysis.files))))
# file.remove(analysis.files)
#
#
# system2(command= "java",
# args = c(paste0("-Xmx4g"),
# paste0("-Xms3g"),
# paste0("-jar ",mixcr.path), "analyze","help" ))
#
# targets <- openxlsx::read.xlsx("/media/respaldo4t/Consultorias/Montes/mouse/TablaURLS.xlsx")
# log.file <- "/media/respaldo4t/Consultorias/Montes/mouse/TablaURLS.xlsx"
# lapply(1:nrow(targets), function(id){
# fileID1 <- rev(unlist(stringr::str_split(targets$url1[id],"/")))[2]
# fileID2 <- rev(unlist(stringr::str_split(targets$url2[id],"/")))[2]
# fileOUT <- targets$Name[id]
# cat(paste0("\n-----------------" ))
# cat(paste0("\n",fileID1, ": R1" ))
# arg2 <- paste0("wget --load-cookies /tmp/cookies.txt \"https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=FILEID' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\\1\\n/p'",")","&id=FILEID\"")
# arg2 <- stringr::str_replace_all(arg2, "FILEID",fileID1)
# arg2 <- paste(arg2," -O ",paste0("/media/respaldo4t/Consultorias/Montes/mouse/","D120T",fileOUT,".R1.fastq.gz")," && rm -rf /tmp/cookies.txt")
# system(command = arg2, ignore.stdout = TRUE)
# cat(paste0("\n",fileID1, ": R2" ))
#
# arg2 <- paste0("wget --load-cookies /tmp/cookies.txt \"https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=FILEID' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\\1\\n/p'",")","&id=FILEID\"")
# arg2 <- stringr::str_replace_all(arg2, "FILEID",fileID2)
# arg2 <- paste(arg2," -O ",paste0("/media/respaldo4t/Consultorias/Montes/mouse/","D120T",fileOUT,".R2.fastq.gz")," && rm -rf /tmp/cookies.txt")
# system(command = arg2, ignore.stdout = TRUE)
#
# })
mixcr.path <- "/media/respaldo4t/mixcr3/mixcr.jar"
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar align --species hsa --chains TCR --parameters rna-seq -OallowPartialAlignments=true --threads 8 ${INPUT_FASTQ}.R1.fastq.gz ${INPUT_FASTQ}.R2.fastq.gz ${OUTPUT_FILE}.alignments.vdjca
species <- "mmu"#hsa for human
nThreads <- 6
file1 <- "/media/respaldo4t/Consultorias/Montes/mouse/D120T33.R1.fastq.gz"
file2 <- stringr::str_replace(file1,".R1.fasta",".R2.fasta")
align.ofile <- file.path(dirname(file1), paste0(basename(file1),".alignments.vdjca"))
base.args <- c(paste0("-Xmx4g"),paste0("-Xms3g"),paste0("-jar ",mixcr.path))
RunMiXCR <- function(sbj, species = c("hsa","mmu"), nTreads){
software <- RMiXCR:::.OpenConfigFile()
cat(paste0("\nAlignment"))
if(missing(nTreads)){
nt <- parallel::detectCores()
nTreads <- ifelse(nt-2 < 1, 1, nt)
message(paste0("\nRunning with ", nt, " Cores"))
}
species <- match.arg(species, c("hsa","mmu") )
file1 <- sbj
file2 <- stringr::str_replace(file1,".R1.fasta",".R2.fasta")
align.ofile <- file.path(dirname(file1), paste0(basename(file1),".alignments.vdjca"))
system2(command= "java",
args = c(software$mixcr$base.args,"align",
paste0("--species ",species),
"--chains TCR",
"--parameters rna-seq",
"-OallowPartialAlignments=true",
paste0("--threads ",nThreads),
file1,
file2,
align.ofile))
if(file.exists(align.ofile)==FALSE){
stop(align.ofile)
}
assemble.ofile <- file.path(dirname(file1), paste0(basename(file1),".clones.clns"))
cat(paste0("\nAssembling"))
system2(command = "java",
args = c(software$mixcr$base.args,
"assemble",
paste0("--threads ",nThreads),
"-OmaxBadPointsPercent=0",
align.ofile,
assemble.ofile
))
if(file.exists(assemble.ofile)==FALSE){
stop(assemble.ofile)
}
cat(paste0("\nExporting clones to Excel file"))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "--chains TCR",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR -p min ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.vmin.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "--chains TCR",
"-p min",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns","vmin.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.vdetails.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "-count",
"-vhit", "-dhit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".vdetails.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRA -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRA.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRA", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRA.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRB -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRB.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRB", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRB.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRG -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRG.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRG", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRG.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRD -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRD.clones.txt
system2(command = "java",
args = c(software$mixcr$base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRD", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRD.clones.tab")
))
to.excel <- lapply(c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab"), function(x){
if(file.exists(stringr::str_replace(assemble.ofile,".clns",x))){
return(read.table(stringr::str_replace(assemble.ofile,".clns",x),h=T, sep="\t"))
}else{
return(NA)
}
})
aux.files.subfix <- c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab")
names(to.excel) <- stringr::str_remove(c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab"),".tab")
openxlsx::write.xlsx(to.excel, stringr::str_replace(assemble.ofile,".clns",".xlsx"))
file.remove(stringr::str_replace(assemble.ofile,".clns",aux.files.subfix))
return(invisible(aux.files.subfix))
}
cat(paste0("\nAlignment"))
system2(command= "java",
args = c(base.args,"align",
paste0("--species ",species),
"--chains TCR",
"--parameters rna-seq",
"-OallowPartialAlignments=true",
paste0("--threads ",nThreads),
file1,
file2,
align.ofile))
if(file.exists(align.ofile)==FALSE){
stop(align.ofile)
}
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar assemble --threads 8 -OmaxBadPointsPercent=0 ${OUTPUT_FILE}.alignments.vdjca ${OUTPUT_FILE}.clones.clns
assemble.ofile <- file.path(dirname(file1), paste0(basename(file1),".clones.clns"))
cat(paste0("\nAssembling"))
system2(command = "java",
args = c(base.args,
"assemble",
paste0("--threads ",nThreads),
"-OmaxBadPointsPercent=0",
align.ofile,
assemble.ofile
))
if(file.exists(assemble.ofile)==FALSE){
stop(assemble.ofile)
}
#Exporting clones to tab-delimited file
cat(paste0("\nExporting clones to tab-delimited file"))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "--chains TCR",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR -p min ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.vmin.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "--chains TCR",
"-p min",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns","vmin.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.vdetails.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "-count",
"-vhit", "-dhit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".vdetails.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRA -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRA.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRA", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRA.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRB -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRB.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRB", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRB.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRG -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRG.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRG", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRG.clones.tab")
))
# java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRD -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRD.clones.txt
system2(command = "java",
args = c(base.args,
"exportClones", "-count",
"-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
"-nFeature CDR3", "-c TRD", "-aaFeature CDR3",
assemble.ofile,
stringr::str_replace(assemble.ofile,".clns",".TRD.clones.tab")
))
to.excel <- lapply(c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab"), function(x){
if(file.exists(stringr::str_replace(assemble.ofile,".clns",x))){
return(read.table(stringr::str_replace(assemble.ofile,".clns",x),h=T, sep="\t"))
}else{
return(NA)
}
})
aux.files.subfix <- c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab")
names(to.excel) <- stringr::str_remove(c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab"),".tab")
openxlsx::write.xlsx(to.excel, stringr::str_replace(assemble.ofile,".clns",".xlsx"))
file.remove(stringr::str_replace(assemble.ofile,".clns",aux.files.subfix))
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