R/scSamToBam.R
In wzthu/ATACFlow: An Easy-to-use Systematic pipeline for ATACseq data analysis
Defines functions
scSam2bam
Documented in
scSam2bam
setClass(Class = "SCSamToBam",
contains = "ATACProc"
)
setMethod(
f = "init",
signature = "SCSamToBam",
definition = function(.Object,prevSteps = list(),...){
atacProc <- NULL
if(length(prevSteps)>0){
atacProc <- prevSteps[[1]]
}
allparam <- list(...)
samInput <- allparam[["samInput"]]
bamOutput <- allparam[["bamOutput"]]
uniqueBamOutput <- allparam[["uniqueBamOutput"]]
statCsvOutput <- allparam[["statCsvOutput"]]
tsvOutput <-allparam[["tsvOutput"]]
isSort <- allparam[["isSort"]]
# necessary parameters
if((!is.null(atacProc)) ){
input(.Object)[["samInput"]] <- getParam(atacProc, "samOutput")
}else if(is.null(atacProc)){ # input
input(.Object)[["samInput"]] <- samInput
}
# unnecessary parameters
if(is.null(bamOutput)){
param(.Object)[["name_tmp"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","" )
output(.Object)[["bamOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","bam")
if(isSort){
output(.Object)[["baiOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","bam.bai")
}
}else{
bamOutput <- addFileSuffix(bamOutput,".bam")
param(.Object)[["name_tmp"]] <- substring(bamOutput,first = 1,last = nchar(bamOutput) - 4)
output(.Object)[["bamOutput"]] <- bamOutput
if(isSort){
output(.Object)[["baiOutput"]] <- addFileSuffix(bamOutput,".bai")
}
}
if(is.null(uniqueBamOutput)){
param(.Object)[["unique_name_tmp"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","unique" )
output(.Object)[["uniqueBamOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","unique.bam")
if(isSort){
output(.Object)[["uniqueBaiOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","unique.bam.bai")
}
}else{
uniqueBamOutput <- addFileSuffix(uniqueBamOutput,".bam")
param(.Object)[["unique_name_tmp"]] <- substring(uniqueBamOutput,first = 1,last = nchar(uniqueBamOutput) - 4)
output(.Object)[["uniqueBamOutput"]] <- uniqueBamOutput
if(isSort){
output(.Object)[["uniqueBaiOutput"]] <- addFileSuffix(bamOutput,".bai")
}
}
if(is.null(statCsvOutput)){
output(.Object)[["statCsvOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","csv")
}
if(is.null(tsvOutput)){
output(.Object)[["tsvOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","stat.tsv")
}
param(.Object)[['isSort']] <- isSort
.Object
}
)
setMethod(
f = "processing",
signature = "SCSamToBam",
definition = function(.Object,...){
samInput <- input(.Object)[["samInput"]]
bamOutput <- output(.Object)[["bamOutput"]]
desOutput <- param(.Object)[["name_tmp"]]
desOutputByBarcode <- paste0(desOutput,'.byBarcode')
uniqueBamOutput <- output(.Object)[["uniqueBamOutput"]]
uniqueDesOutput <- param(.Object)[["unique_name_tmp"]]
statCsvOutput <- output(.Object)[["statCsvOutput"]]
tsvOutput <- output(.Object)[["tsvOutput"]]
isSort <- param(.Object)[["isSort"]]
if(file.exists(bamOutput)){
file.remove(bamOutput)
}
if(file.exists(uniqueBamOutput)){
file.remove(uniqueBamOutput)
}
if(file.exists(tsvOutput)){
file.remove(tsvOutput)
}
if(file.exists(statCsvOutput)){
file.remove(statCsvOutput)
}
Rsamtools::asBam(file = samInput,
destination = desOutput,
overwrite = TRUE, indexDestination = isSort)
Rsamtools::sortBam(file = bamOutput, destination = desOutputByBarcode, byQname=TRUE, maxMemory=15 * 1024)
Rsamtools::asSam(file=paste0(desOutputByBarcode,'.bam'),overwrite=TRUE)
samfile <- file(paste0(desOutputByBarcode,'.sam'),'r')
headLine <- c()
while(TRUE){
lines <- readLines(samfile,n=1)
if(length(lines)==0||!startsWith(lines,'@')){
break
}else{
headLine <- c(headLine,lines)
}
}
lines <- c(lines, readLines(samfile,n=1000000+1))
barcode <- NULL
vec_left_list <- list()
left_lines <- c()
endflag <- FALSE
stat_list <- list()
count <- 1
nb_barcode <- 0
# cl <- makeCluster(20)
while(TRUE){
vec_list <- c(vec_left_list,strsplit(lines, '\t'))
lines <- c(left_lines, lines)
barcodes <- lapply(vec_list,function(x) x[1])
barcodes <- unlist(lapply(strsplit(unlist(barcodes),':'), function(x) x[1]))
bs <- unique(barcodes)
ed <- min(length(bs) - 1,10000)
if(endflag){
ed <- length(bs)
}
nb_barcode <- nb_barcode + ed
print(nb_barcode)
vec_left_list <- vec_list[!(barcodes %in% bs[1:ed])]
left_lines <- lines[!(barcodes %in% bs[1:ed])]
if(ed>=1){
if(Sys.info()[['sysname']]=='Linux' || Sys.info()[['sysname']]=='Darwin'){
stat_rs <- mclapply( 1:ed, function(i){
b <- bs[i]
if(!file.exists(paste0(desOutput,'.',b,'.sam'))){
write(headLine,file = paste0(desOutput,'.',b,'.sam'), append = TRUE, sep = "\n")
}
write(lines[barcodes==b],file = paste0(desOutput,'.',b,'.sam'), append = TRUE, sep = "\n")
asBam(paste0(desOutput,'.',b,'.sam'),overwrite=TRUE)
file.remove(paste0(desOutput,'.',b,'.sam'))
rs <- readGAlignmentPairs(paste0(desOutput,'.',b,'.bam'),param=ScanBamParam(what=scanBamWhat()),use.names = T)
file.remove(paste0(desOutput,'.',b,'.bam'))
file.remove(paste0(desOutput,'.',b,'.bam.bai'))
st1 <- start(first(rs))
ed1 <- end(first(rs))
st2 <- start(second(rs))
ed2 <- end(second(rs))
st <- st1
ed <- ed2
sel1 <- as.logical(strand(first(rs)) == '-')
st[sel1] <- st2[sel1]
ed[sel1] <- st1[sel1]
bed <- paste(rname(first(rs)),st,ed,sep='\t')
sel <- duplicated(bed)
rtracklayer::export(rs[!sel],BamFile(paste0(desOutput,'.',b,'.unique.sam')))
bed1 <- as.data.frame(table(bed))
return(list(tsv=paste(bed1$bed,b, bed1$Freq,sep='\t'),
# bed= rs[!sel],
# bf = BamFile(uniqueBams[i]),
stat=data.frame(barcode=b,
total = length(rs),
duplicate = sum(bed1$Freq>1),
chimeric = sum(mcols(first(rs))$flag==2048 | mcols(second(rs))$flag==2048),
unmapped = sum(mcols(first(rs))$flag==4 | mcols(second(rs))$flag==4),
lowmapq = sum(mcols(first(rs))$mapq < 30 | mcols(second(rs))$mapq < 30),
mitochondrial = sum(rname(first(rs))=='chrM' | rname(second(rs))=='chrM'),
nonprimary = sum(mcols(first(rs))$flag==256 | mcols(second(rs))$flag==256),
passed_filters = sum(!sel))))
},mc.cores=20)
}else{
stat_rs <- lapply( 1:ed, function(i){
b <- bs[i]
if(!file.exists(paste0(desOutput,'.',b,'.sam'))){
write(headLine,file = paste0(desOutput,'.',b,'.sam'), append = TRUE, sep = "\n")
}
write(lines[barcodes==b],file = paste0(desOutput,'.',b,'.sam'), append = TRUE, sep = "\n")
asBam(paste0(desOutput,'.',b,'.sam'),overwrite=TRUE)
file.remove(paste0(desOutput,'.',b,'.sam'))
rs <- readGAlignmentPairs(paste0(desOutput,'.',b,'.bam'),param=ScanBamParam(what=scanBamWhat()),use.names = T)
file.remove(paste0(desOutput,'.',b,'.bam'))
file.remove(paste0(desOutput,'.',b,'.bam.bai'))
st1 <- start(first(rs))
ed1 <- end(first(rs))
st2 <- start(second(rs))
ed2 <- end(second(rs))
st <- st1
ed <- ed2
sel1 <- as.logical(strand(first(rs)) == '-')
st[sel1] <- st2[sel1]
ed[sel1] <- st1[sel1]
bed <- paste(rname(first(rs)),st,ed,sep='\t')
sel <- duplicated(bed)
rtracklayer::export(rs[!sel],BamFile(paste0(desOutput,'.',b,'.unique.sam')))
bed1 <- as.data.frame(table(bed))
# write(paste(bed1$bed,b, bed1$Freq,sep='\t'),file=tsvOutput, sep = "\n")
return(list(tsv=paste(bed1$bed,b, bed1$Freq,sep='\t'),
# bed= rs[!sel],
# bf = BamFile(uniqueBams[i]),
stat=data.frame(barcode=b,
total = length(rs),
duplicate = sum(bed1$Freq>1),
chimeric = sum(mcols(first(rs))$flag==2048 | mcols(second(rs))$flag==2048),
unmapped = sum(mcols(first(rs))$flag==4 | mcols(second(rs))$flag==4),
lowmapq = sum(mcols(first(rs))$mapq < 30 | mcols(second(rs))$mapq < 30),
mitochondrial = sum(rname(first(rs))=='chrM' | rname(second(rs))=='chrM'),
nonprimary = sum(mcols(first(rs))$flag==256 | mcols(second(rs))$flag==256),
passed_filters = sum(!sel))))
})
}
if(ed==1){
file.rename(from=paste0(desOutput,'.',bs[1:ed],'.unique.bam'),to=paste0(desOutput,'.',count,'.unique.bam'))
}else{
mergeBam(files=paste0(desOutput,'.',bs[1:ed],'.unique.bam'),destination=paste0(desOutput,'.',count,'.unique.bam'))
}
file.remove(paste0(desOutput,'.',bs[1:ed],'.unique.bam'))
file.remove(paste0(desOutput,'.',bs[1:ed],'.unique.bam.bai'))
count <- count + 1
tsv <- write(unlist(lapply(stat_rs, function(v){v$tsv})),file=tsvOutput, append = TRUE, sep = "\n")
stat_list <- c(stat_list, lapply(stat_rs, function(v){v$stat}))
}
if(endflag){
break
}
if(length(bs) < 2 * 10000){
lines <- readLines(samfile,n=1000000)
}else{
lines <- readLines(samfile,n=100)
}
if(length(lines)==0 && length(bs) == 0){
break
}
if(length(lines)==0 && length(bs) < 2*10000){
endflag <- TRUE
}
}
Rsamtools::mergeBam(files=paste0(desOutput,'.',1:(count-1),'.unique.bam'), destination=uniqueBamOutput,overwrite = TRUE)
Rsamtools::indexBam(file=uniqueBamOutput)
write.csv(do.call(rbind,stat_list),file=statCsvOutput,quote = FALSE, row.names=FALSE)
file.remove(paste0(desOutput,'.',1:(count-1),'.unique.bam'))
.Object
}
)
setMethod(
f = "genReport",
signature = "SCSamToBam",
definition = function(.Object, ...){
.Object
}
)
#' @name SCSamToBam
#' @title Convert sam format to bam format.
#' @description
#' This function convert a sam file into a bam file.
#' @param atacProc \code{\link{ATACProc-class}} object scalar.
#' It has to be the return value of upstream process:
#' \code{\link{atacBowtie2Mapping}}.
#' @param samInput \code{Character} scalar.
#' Sam file input path.
#' @param bamOutput \code{Character} scalar.
#' Bam file output path. If ignored, bed file will be put in the same path as
#' the sam file.
#' @param isSort \code{Logical} scalar.
#' Sort bam.
#' @param ... Additional arguments, currently unused.
#' @details The parameter related to input and output file path
#' will be automatically
#' obtained from \code{\link{ATACProc-class}} object(\code{atacProc}) or
#' generated based on known parameters
#' if their values are default(e.g. \code{NULL}).
#' Otherwise, the generated values will be overwrited.
#' If you want to use this function independently,
#' you can use \code{bamToBed} instead.
#' @return An invisible \code{\link{ATACProc-class}} object scalar for
#' downstream analysis.
#' @author Wei Zhang
#' @examples
#'
#' library(R.utils)
#' sam_bz <- system.file("extdata", "Example.sam.bz2", package="esATAC")
#' sam_path <- as.vector(bunzip2(filename = sam_bz,
#' destname = file.path(getwd(), "Example.sam"),
#' ext="bz2", FUN=bzfile, remove = FALSE))
#' sam2bam(samInput = sam_path)
#'
#' @seealso
#' \code{\link{atacBowtie2Mapping}}
#' \code{\link{atacBam2Bed}}
#' \code{\link{atacBamSort}}
setGeneric("atacSCSam2Bam",function(atacProc,
samInput = NULL, bamOutput = NULL,uniqueBamOutput = NULL, tsvOutput = NULL, statCsvOutput = NULL, isSort=TRUE, ...) standardGeneric("atacSCSam2Bam"))
#' @rdname SCSamToBam
#' @aliases atacSCSam2Bam
#' @export
setMethod(
f = "atacSCSam2Bam",
signature = "ATACProc",
definition = function(atacProc,
samInput = NULL, bamOutput = NULL, uniqueBamOutput = NULL, tsvOutput = NULL, statCsvOutput = NULL,isSort=TRUE, ...){
allpara <- c(list(Class = "SCSamToBam", prevSteps = list(atacProc)),as.list(environment()),list(...))
step <- do.call(new,allpara)
invisible(step)
}
)
#' @rdname SCSamToBam
#' @aliases scSam2bam
#' @export
scSam2bam <- function(samInput, bamOutput = NULL, uniqueBamOutput = NULL, tsvOutput = NULL, statCsvOutput = NULL, isSort=TRUE, ...){
allpara <- c(list(Class = "SCSamToBam", prevSteps = list()),as.list(environment()),list(...))
step <- do.call(new,allpara)
invisible(step)
}
wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.
R Package Documentation
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Defines functions scSam2bam
Documented in scSam2bam
setClass(Class = "SCSamToBam",
contains = "ATACProc"
)
setMethod(
f = "init",
signature = "SCSamToBam",
definition = function(.Object,prevSteps = list(),...){
atacProc <- NULL
if(length(prevSteps)>0){
atacProc <- prevSteps[[1]]
}
allparam <- list(...)
samInput <- allparam[["samInput"]]
bamOutput <- allparam[["bamOutput"]]
uniqueBamOutput <- allparam[["uniqueBamOutput"]]
statCsvOutput <- allparam[["statCsvOutput"]]
tsvOutput <-allparam[["tsvOutput"]]
isSort <- allparam[["isSort"]]
# necessary parameters
if((!is.null(atacProc)) ){
input(.Object)[["samInput"]] <- getParam(atacProc, "samOutput")
}else if(is.null(atacProc)){ # input
input(.Object)[["samInput"]] <- samInput
}
# unnecessary parameters
if(is.null(bamOutput)){
param(.Object)[["name_tmp"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","" )
output(.Object)[["bamOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","bam")
if(isSort){
output(.Object)[["baiOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","bam.bai")
}
}else{
bamOutput <- addFileSuffix(bamOutput,".bam")
param(.Object)[["name_tmp"]] <- substring(bamOutput,first = 1,last = nchar(bamOutput) - 4)
output(.Object)[["bamOutput"]] <- bamOutput
if(isSort){
output(.Object)[["baiOutput"]] <- addFileSuffix(bamOutput,".bai")
}
}
if(is.null(uniqueBamOutput)){
param(.Object)[["unique_name_tmp"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","unique" )
output(.Object)[["uniqueBamOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","unique.bam")
if(isSort){
output(.Object)[["uniqueBaiOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","unique.bam.bai")
}
}else{
uniqueBamOutput <- addFileSuffix(uniqueBamOutput,".bam")
param(.Object)[["unique_name_tmp"]] <- substring(uniqueBamOutput,first = 1,last = nchar(uniqueBamOutput) - 4)
output(.Object)[["uniqueBamOutput"]] <- uniqueBamOutput
if(isSort){
output(.Object)[["uniqueBaiOutput"]] <- addFileSuffix(bamOutput,".bai")
}
}
if(is.null(statCsvOutput)){
output(.Object)[["statCsvOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","csv")
}
if(is.null(tsvOutput)){
output(.Object)[["tsvOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","stat.tsv")
}
param(.Object)[['isSort']] <- isSort
.Object
}
)
setMethod(
f = "processing",
signature = "SCSamToBam",
definition = function(.Object,...){
samInput <- input(.Object)[["samInput"]]
bamOutput <- output(.Object)[["bamOutput"]]
desOutput <- param(.Object)[["name_tmp"]]
desOutputByBarcode <- paste0(desOutput,'.byBarcode')
uniqueBamOutput <- output(.Object)[["uniqueBamOutput"]]
uniqueDesOutput <- param(.Object)[["unique_name_tmp"]]
statCsvOutput <- output(.Object)[["statCsvOutput"]]
tsvOutput <- output(.Object)[["tsvOutput"]]
isSort <- param(.Object)[["isSort"]]
if(file.exists(bamOutput)){
file.remove(bamOutput)
}
if(file.exists(uniqueBamOutput)){
file.remove(uniqueBamOutput)
}
if(file.exists(tsvOutput)){
file.remove(tsvOutput)
}
if(file.exists(statCsvOutput)){
file.remove(statCsvOutput)
}
Rsamtools::asBam(file = samInput,
destination = desOutput,
overwrite = TRUE, indexDestination = isSort)
Rsamtools::sortBam(file = bamOutput, destination = desOutputByBarcode, byQname=TRUE, maxMemory=15 * 1024)
Rsamtools::asSam(file=paste0(desOutputByBarcode,'.bam'),overwrite=TRUE)
samfile <- file(paste0(desOutputByBarcode,'.sam'),'r')
headLine <- c()
while(TRUE){
lines <- readLines(samfile,n=1)
if(length(lines)==0||!startsWith(lines,'@')){
break
}else{
headLine <- c(headLine,lines)
}
}
lines <- c(lines, readLines(samfile,n=1000000+1))
barcode <- NULL
vec_left_list <- list()
left_lines <- c()
endflag <- FALSE
stat_list <- list()
count <- 1
nb_barcode <- 0
# cl <- makeCluster(20)
while(TRUE){
vec_list <- c(vec_left_list,strsplit(lines, '\t'))
lines <- c(left_lines, lines)
barcodes <- lapply(vec_list,function(x) x[1])
barcodes <- unlist(lapply(strsplit(unlist(barcodes),':'), function(x) x[1]))
bs <- unique(barcodes)
ed <- min(length(bs) - 1,10000)
if(endflag){
ed <- length(bs)
}
nb_barcode <- nb_barcode + ed
print(nb_barcode)
vec_left_list <- vec_list[!(barcodes %in% bs[1:ed])]
left_lines <- lines[!(barcodes %in% bs[1:ed])]
if(ed>=1){
if(Sys.info()[['sysname']]=='Linux' || Sys.info()[['sysname']]=='Darwin'){
stat_rs <- mclapply( 1:ed, function(i){
b <- bs[i]
if(!file.exists(paste0(desOutput,'.',b,'.sam'))){
write(headLine,file = paste0(desOutput,'.',b,'.sam'), append = TRUE, sep = "\n")
}
write(lines[barcodes==b],file = paste0(desOutput,'.',b,'.sam'), append = TRUE, sep = "\n")
asBam(paste0(desOutput,'.',b,'.sam'),overwrite=TRUE)
file.remove(paste0(desOutput,'.',b,'.sam'))
rs <- readGAlignmentPairs(paste0(desOutput,'.',b,'.bam'),param=ScanBamParam(what=scanBamWhat()),use.names = T)
file.remove(paste0(desOutput,'.',b,'.bam'))
file.remove(paste0(desOutput,'.',b,'.bam.bai'))
st1 <- start(first(rs))
ed1 <- end(first(rs))
st2 <- start(second(rs))
ed2 <- end(second(rs))
st <- st1
ed <- ed2
sel1 <- as.logical(strand(first(rs)) == '-')
st[sel1] <- st2[sel1]
ed[sel1] <- st1[sel1]
bed <- paste(rname(first(rs)),st,ed,sep='\t')
sel <- duplicated(bed)
rtracklayer::export(rs[!sel],BamFile(paste0(desOutput,'.',b,'.unique.sam')))
bed1 <- as.data.frame(table(bed))
return(list(tsv=paste(bed1$bed,b, bed1$Freq,sep='\t'),
# bed= rs[!sel],
# bf = BamFile(uniqueBams[i]),
stat=data.frame(barcode=b,
total = length(rs),
duplicate = sum(bed1$Freq>1),
chimeric = sum(mcols(first(rs))$flag==2048 | mcols(second(rs))$flag==2048),
unmapped = sum(mcols(first(rs))$flag==4 | mcols(second(rs))$flag==4),
lowmapq = sum(mcols(first(rs))$mapq < 30 | mcols(second(rs))$mapq < 30),
mitochondrial = sum(rname(first(rs))=='chrM' | rname(second(rs))=='chrM'),
nonprimary = sum(mcols(first(rs))$flag==256 | mcols(second(rs))$flag==256),
passed_filters = sum(!sel))))
},mc.cores=20)
}else{
stat_rs <- lapply( 1:ed, function(i){
b <- bs[i]
if(!file.exists(paste0(desOutput,'.',b,'.sam'))){
write(headLine,file = paste0(desOutput,'.',b,'.sam'), append = TRUE, sep = "\n")
}
write(lines[barcodes==b],file = paste0(desOutput,'.',b,'.sam'), append = TRUE, sep = "\n")
asBam(paste0(desOutput,'.',b,'.sam'),overwrite=TRUE)
file.remove(paste0(desOutput,'.',b,'.sam'))
rs <- readGAlignmentPairs(paste0(desOutput,'.',b,'.bam'),param=ScanBamParam(what=scanBamWhat()),use.names = T)
file.remove(paste0(desOutput,'.',b,'.bam'))
file.remove(paste0(desOutput,'.',b,'.bam.bai'))
st1 <- start(first(rs))
ed1 <- end(first(rs))
st2 <- start(second(rs))
ed2 <- end(second(rs))
st <- st1
ed <- ed2
sel1 <- as.logical(strand(first(rs)) == '-')
st[sel1] <- st2[sel1]
ed[sel1] <- st1[sel1]
bed <- paste(rname(first(rs)),st,ed,sep='\t')
sel <- duplicated(bed)
rtracklayer::export(rs[!sel],BamFile(paste0(desOutput,'.',b,'.unique.sam')))
bed1 <- as.data.frame(table(bed))
# write(paste(bed1$bed,b, bed1$Freq,sep='\t'),file=tsvOutput, sep = "\n")
return(list(tsv=paste(bed1$bed,b, bed1$Freq,sep='\t'),
# bed= rs[!sel],
# bf = BamFile(uniqueBams[i]),
stat=data.frame(barcode=b,
total = length(rs),
duplicate = sum(bed1$Freq>1),
chimeric = sum(mcols(first(rs))$flag==2048 | mcols(second(rs))$flag==2048),
unmapped = sum(mcols(first(rs))$flag==4 | mcols(second(rs))$flag==4),
lowmapq = sum(mcols(first(rs))$mapq < 30 | mcols(second(rs))$mapq < 30),
mitochondrial = sum(rname(first(rs))=='chrM' | rname(second(rs))=='chrM'),
nonprimary = sum(mcols(first(rs))$flag==256 | mcols(second(rs))$flag==256),
passed_filters = sum(!sel))))
})
}
if(ed==1){
file.rename(from=paste0(desOutput,'.',bs[1:ed],'.unique.bam'),to=paste0(desOutput,'.',count,'.unique.bam'))
}else{
mergeBam(files=paste0(desOutput,'.',bs[1:ed],'.unique.bam'),destination=paste0(desOutput,'.',count,'.unique.bam'))
}
file.remove(paste0(desOutput,'.',bs[1:ed],'.unique.bam'))
file.remove(paste0(desOutput,'.',bs[1:ed],'.unique.bam.bai'))
count <- count + 1
tsv <- write(unlist(lapply(stat_rs, function(v){v$tsv})),file=tsvOutput, append = TRUE, sep = "\n")
stat_list <- c(stat_list, lapply(stat_rs, function(v){v$stat}))
}
if(endflag){
break
}
if(length(bs) < 2 * 10000){
lines <- readLines(samfile,n=1000000)
}else{
lines <- readLines(samfile,n=100)
}
if(length(lines)==0 && length(bs) == 0){
break
}
if(length(lines)==0 && length(bs) < 2*10000){
endflag <- TRUE
}
}
Rsamtools::mergeBam(files=paste0(desOutput,'.',1:(count-1),'.unique.bam'), destination=uniqueBamOutput,overwrite = TRUE)
Rsamtools::indexBam(file=uniqueBamOutput)
write.csv(do.call(rbind,stat_list),file=statCsvOutput,quote = FALSE, row.names=FALSE)
file.remove(paste0(desOutput,'.',1:(count-1),'.unique.bam'))
.Object
}
)
setMethod(
f = "genReport",
signature = "SCSamToBam",
definition = function(.Object, ...){
.Object
}
)
#' @name SCSamToBam
#' @title Convert sam format to bam format.
#' @description
#' This function convert a sam file into a bam file.
#' @param atacProc \code{\link{ATACProc-class}} object scalar.
#' It has to be the return value of upstream process:
#' \code{\link{atacBowtie2Mapping}}.
#' @param samInput \code{Character} scalar.
#' Sam file input path.
#' @param bamOutput \code{Character} scalar.
#' Bam file output path. If ignored, bed file will be put in the same path as
#' the sam file.
#' @param isSort \code{Logical} scalar.
#' Sort bam.
#' @param ... Additional arguments, currently unused.
#' @details The parameter related to input and output file path
#' will be automatically
#' obtained from \code{\link{ATACProc-class}} object(\code{atacProc}) or
#' generated based on known parameters
#' if their values are default(e.g. \code{NULL}).
#' Otherwise, the generated values will be overwrited.
#' If you want to use this function independently,
#' you can use \code{bamToBed} instead.
#' @return An invisible \code{\link{ATACProc-class}} object scalar for
#' downstream analysis.
#' @author Wei Zhang
#' @examples
#'
#' library(R.utils)
#' sam_bz <- system.file("extdata", "Example.sam.bz2", package="esATAC")
#' sam_path <- as.vector(bunzip2(filename = sam_bz,
#' destname = file.path(getwd(), "Example.sam"),
#' ext="bz2", FUN=bzfile, remove = FALSE))
#' sam2bam(samInput = sam_path)
#'
#' @seealso
#' \code{\link{atacBowtie2Mapping}}
#' \code{\link{atacBam2Bed}}
#' \code{\link{atacBamSort}}
setGeneric("atacSCSam2Bam",function(atacProc,
samInput = NULL, bamOutput = NULL,uniqueBamOutput = NULL, tsvOutput = NULL, statCsvOutput = NULL, isSort=TRUE, ...) standardGeneric("atacSCSam2Bam"))
#' @rdname SCSamToBam
#' @aliases atacSCSam2Bam
#' @export
setMethod(
f = "atacSCSam2Bam",
signature = "ATACProc",
definition = function(atacProc,
samInput = NULL, bamOutput = NULL, uniqueBamOutput = NULL, tsvOutput = NULL, statCsvOutput = NULL,isSort=TRUE, ...){
allpara <- c(list(Class = "SCSamToBam", prevSteps = list(atacProc)),as.list(environment()),list(...))
step <- do.call(new,allpara)
invisible(step)
}
)
#' @rdname SCSamToBam
#' @aliases scSam2bam
#' @export
scSam2bam <- function(samInput, bamOutput = NULL, uniqueBamOutput = NULL, tsvOutput = NULL, statCsvOutput = NULL, isSort=TRUE, ...){
allpara <- c(list(Class = "SCSamToBam", prevSteps = list()),as.list(environment()),list(...))
step <- do.call(new,allpara)
invisible(step)
}
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