我有一个R脚本,可以读取.sam文件中的行,这是在映射后的结果。为了更容易地操作它们并创建我需要的wig文件,或者计算我需要的cov3和cov5,我想将sam文件的行解析成字符串。请问如何让我的脚本运行更快?如何更快地将大型.sam文件的行解析成数据框?以下是我的脚本:
gc()
rm(list=ls())
exptPath <- "/home/dimitris/INDEX3PerfectUnique31cov5.sam"
lines <- readLines(exptPath)
pos = lines
pos
chrom = lines
chrom
pos = ""
chrom = ""
nn = length(lines)
nn
# parse lines of sam file into strings(this part is very very slow)
rr = strsplit(lines,"\t", fixed = TRUE)
rr
trr = do.call(rbind.data.frame, rr)
pos = as.numeric(as.character(trr[8:nn,4]))
# for cov3
#pos = pos+25
#pos
chrom = trr[8:nn,3]
pos = as.numeric(pos)
pos
tab1 = table(chrom,pos, exclude="")
tab1
ftab1 = as.data.frame(tab1)
ftab1 = subset(ftab1, ftab1[3] != 0)
ftab1 = subset(ftab1, ftab1[1] != "<NA>")
oftab1 = ftab1[ order(ftab1[,1]), ]
final.ftab1 = oftab1[,2:3]
write.table(final.ftab1, "ind3_cov5_wig.txt", row.names=FALSE,
sep=" ", quote=FALSE)