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#
# pliu 20150509
#
# module for processing ChIP-seq data
#
main <- function() {
name2func <- list(
'guessFqEncoding' = guessFqEncoding
)
argv <- commandArgs(trailingOnly=T)
name2func[[argv[1]]](argv[2:length(argv)])
}
guessFqEncoding <- function(argv){
.libPaths(c(argv[4], .libPaths()))
suppressMessages(library(data.table))
suppressMessages(library(ShortRead))
nthr <- strtoi(argv[1])
s_infiles <- argv[2]
fout <- argv[3]
files <- strsplit(s_infiles, ',', fixed=T)[[1]]
#lapply(files, guessFqEncodingByFile)
## cannot use mclapply here, ShortRead::qa function bound with BiocParallel
## have to use bplapply and define single core when call qa
## this new feature only appear in the new version of ShortRead
register(MulticoreParam(workers=nthr))
outdt <- rbindlist(bplapply(files, guessFqEncodingByFile))
write.table(outdt, fout, sep="\t", quote=F, col.names=T, row.names=F)
#cat('File written:', fout, "\n")
}
## exam and guess Fastq's quality score's format
guessFqEncodingByFile <- function(fq) {
qual <- qa(fq, BPPARAM=registered()$SerialParam)
bq <- qual[['baseQuality']]
score <- subset(bq, bq$count > 0, select=c('score'))$score
encod <- 'unknown'
if ( any( strsplit(intToUtf8(33:58), '')[[1]] %in% score ) ) {
encod <- '--phred33-quals'
} else if ( any( strsplit(intToUtf8(59:64), '')[[1]] %in% score ) ) {
#encod <- 'solexa ver. <1.3'
encod <- '--solexa-quals'
} else if ( any( strsplit(intToUtf8(75:104), '')[[1]] %in% score ) ) {
encod <- '--phred64-quals'
}
return(list(file=fq, encoding=encod))
}
main()
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