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Jeremiah Wala
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Jul 7, 2015
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| library(optparse) | ||
| #RLIBDIR = '/cga/meyerson/home/marcin/Software/R/x86_64-unknown-linux-gnu-library/3.1/' | ||
| #GIT.HOME = '/cga/meyerson/home/marcin/DB/git' | ||
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| option_list = list( | ||
| make_option(c("-i", "--input"), type = "character", default = "qcreport.txt", help = "Input txt file from a snowman preprocess qcreport.txt"), | ||
| make_option(c("-o", "--output"), type = "character", default = "qcreport.pdf", help = "Output pdf to generate") | ||
| ) | ||
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| parseobj = OptionParser(option_list=option_list) | ||
| opt = parse_args(parseobj) | ||
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| if (is.null(opt$input)) | ||
| stop(print_help(parseobj)) | ||
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| print(getwd()) | ||
| if (!file.exists(opt$input)) | ||
| stop(paste("Input file does not exist", opt$input)) | ||
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| print(opt) | ||
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| require(ggplot2) | ||
| require(reshape2) | ||
| require(gridExtra) | ||
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| ## read the table | ||
| con <- file(opt$input, open = "r") | ||
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| df.mapq <- df.nm <- df.isize <- df.as <- df.xp <- df.len <- df.phred <- df.clip <- data.frame() | ||
| rg <- list() | ||
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| ## function for parsing histogram strings | ||
| function(ll, id) { | ||
| ss <- strsplit(ll[id],',')[[1]] | ||
| df <- data.frame(matrix(unlist(strsplit(ss, '_')), nrow=length(ss), byrow=T)) | ||
| colnames(df) <- c("Min", "Max", "Count") | ||
| return (df) | ||
| } | ||
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| while (length(line <- readLines(con, n = 1, warn = FALSE)) > 0) { | ||
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| ll <- strsplit(line, '\t')[[1]] | ||
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| thisrg = ll[1] | ||
| rg[[thisrg]] <- data.frame(readgroup = thisrg, ReadCount = as.numeric(ll[2]), Supplementary = as.numeric(ll[3]), | ||
| Unmapped = as.numeric(ll[4]), MateUnmapped = as.numeric(ll[5]), | ||
| QCFailed = as.numeric(ll[6]), Duplicate = as.numeric(ll[7])) | ||
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| ss <- strsplit(ll[8],',')[[1]] | ||
| df.mapq <- data.frame(matrix(unlist(strsplit(ss, '_')), nrow=length(ss), byrow=T)) | ||
| colnames(df.mapq) <- c("Min", "Max", "Count") | ||
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| ## found a new one | ||
| #if (grepl("ReadGroup", line)) { | ||
| # thisrg = gsub("READGROUP:BI:(.*)", "\\1", line) | ||
| # rg[[thisrg]] <- data.frame(readgroup = thisrg) | ||
| #} else if (grepl("total", line)) { | ||
| # rg[[thisrg]]$total = as.numeric(gsub("total,([0-9]+)", "\\1", line)) | ||
| #} else if (grepl("unmap", line)) { | ||
| # rg[[thisrg]]$unmap = as.numeric(gsub("unmap,([0-9]+)", "\\1", line)) | ||
| #} else if (grepl("qcfail", line)) { | ||
| # rg[[thisrg]]$qcfail = as.numeric(gsub("qcfail,([0-9]+)", "\\1", line)) | ||
| #} else if (grepl("duplicate", line)) { | ||
| # rg[[thisrg]]$duplicate = as.numeric(gsub("duplicate,([0-9]+)", "\\1", line)) | ||
| #} else if (grepl("supplementary", line)) { | ||
| # rg[[thisrg]]$supp = as.numeric(gsub("supplementary,([0-9]+)", "\\1", line)) | ||
| #} else if (grepl("mapq", line)) { | ||
| # df.mapq <- rbind(df.mapq, as.numeric(strsplit(gsub("mapq,([0-9]+)", "\\1", line), ",")[[1]])) | ||
| #} else if (grepl("nm", line)) { | ||
| # df.nm <- rbind(df.nm, as.numeric(strsplit(gsub("nm,([0-9]+)", "\\1", line), ",")[[1]])) | ||
| #} else if (grepl("isize", line)) { | ||
| # df.isize <- rbind(df.isize, as.numeric(strsplit(gsub("isize,([0-9]+)", "\\1", line), ",")[[1]])) | ||
| #} else if (grepl("as", line)) { | ||
| # df.as <- rbind(df.as, as.numeric(strsplit(gsub("as,([0-9]+)", "\\1", line), ",")[[1]])) | ||
| #} else if (grepl("xp", line)) { | ||
| # df.xp <- rbind(df.xp, as.numeric(strsplit(gsub("xp,([0-9]+)", "\\1", line), ",")[[1]])) | ||
| #} else if (grepl("clip", line)) { | ||
| # df.clip <- rbind(df.clip, as.numeric(strsplit(gsub("clip,([0-9]+)", "\\1", line), ",")[[1]])) | ||
| #} else if (grepl("len", line)) { | ||
| # df.len <- rbind(df.len, as.numeric(strsplit(gsub("len,([0-9]+)", "\\1", line), ",")[[1]])) | ||
| #} else if (grepl("phred", line)) { | ||
| # df.phred <- rbind(df.phred, as.numeric(strsplit(gsub("phred,([0-9]+)", "\\1", line), ",")[[1]])) | ||
| #} else { | ||
| # stop(paste("Failed to read file at line:", line)) | ||
| #} | ||
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| } | ||
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| close(con) | ||
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| colnames(df.mapq) <- seq(from=0,to=60) | ||
| colnames(df.nm) <- seq(from=0,to=ncol(df.nm)-1) | ||
| colnames(df.isize) <- seq(from=0,to=ncol(df.isize)-1) | ||
| colnames(df.xp) <- seq(from=0, to=ncol(df.xp)-1) | ||
| colnames(df.as) <- seq(from=0, to=ncol(df.as)-1) | ||
| colnames(df.len) <- seq(from=0, to=ncol(df.len)-1) | ||
| colnames(df.phred) <- seq(from=0, to=ncol(df.phred)-1) | ||
| colnames(df.clip) <- seq(from=0, to=ncol(df.clip)-1) | ||
| readg <- sapply(rg, function(x) x$readgroup) | ||
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| df.mapq$readgroup <- readg | ||
| df.nm$readgroup <- readg | ||
| df.isize$readgroup <- readg | ||
| df.xp$readgroup <- readg | ||
| df.as$readgroup <- readg | ||
| df.phred$readgroup <- readg | ||
| df.len$readgroup <- readg | ||
| df.clip$readgroup <- readg | ||
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| g.mapq <- ggplot(df.mapq.m <- melt(df.mapq, id='readgroup'), aes(x=as.numeric(variable), y=pmax(log(value,10),0), group=readgroup, color=readgroup)) + geom_line() + theme_bw() + scale_x_continuous(limits=c(30,61)) + ylab('Reads') + xlab('Mapping Quality') + scale_y_continuous(breaks=seq(0,8), labels=parse(text=paste('10', seq(0,8), sep='^'))) | ||
| g.nm <- ggplot(df.nm.m <- melt(df.nm, id='readgroup'), aes(x=as.numeric(variable), y=pmax(log(value,10),0), group=readgroup, color=readgroup)) + geom_line() + theme_bw() + scale_x_continuous(limits=c(0,50)) + ylab('Reads') + xlab('NM Tag') + scale_y_continuous(breaks=seq(0,8), labels=parse(text=paste('10', seq(0,8), sep='^'))) | ||
| g.isize <- ggplot(df.isize.m <- melt(df.isize, id='readgroup'), aes(x=as.numeric(variable), y=pmax(log(value,10),0), group=readgroup, color=readgroup)) + geom_line() + theme_bw() + scale_x_continuous(limits=c(10,2001)) + ylab('Reads') + xlab('InsertSize') + scale_y_continuous(breaks=seq(0,8), labels=parse(text=paste('10', seq(0,8), sep='^'))) | ||
| g.xp <- ggplot(df.xp.m <- melt(df.xp, id='readgroup'), aes(x=as.numeric(variable), y=pmax(log(value,10),0), group=readgroup, color=readgroup)) + geom_line() + theme_bw() + scale_x_continuous(limits=c(0,100)) + ylab('Reads') + xlab('XP Tag') + scale_y_continuous(breaks=seq(0,8), labels=parse(text=paste('10', seq(0,8), sep='^'))) | ||
| g.as <- ggplot(df.as.m <- melt(df.as, id='readgroup'), aes(x=as.numeric(variable), y=pmax(log(value,10),0), group=readgroup, color=readgroup)) + geom_line() + theme_bw() + scale_x_continuous(limits=c(0,100)) + ylab('Reads') + xlab('AS Tag') + scale_y_continuous(breaks=seq(0,8), labels=parse(text=paste('10', seq(0,8), sep='^'))) | ||
| g.len <- ggplot(df.len.m <- melt(df.len, id='readgroup'), aes(x=as.numeric(variable), y=pmax(log(value,10),0), group=readgroup, color=readgroup)) + geom_line() + theme_bw() + scale_x_continuous(limits=c(20,102)) + ylab('Reads') + xlab('Read Length') + scale_y_continuous(breaks=seq(0,8), labels=parse(text=paste('10', seq(0,8), sep='^'))) | ||
| g.clip <- ggplot(df.clip.m <- melt(df.clip, id='readgroup'), aes(x=as.numeric(variable), y=pmax(log(value,10),0), group=readgroup, color=readgroup)) + geom_line() + theme_bw() + scale_x_continuous(limits=c(0,85)) + ylab('Reads') + xlab('Clipped bases') + scale_y_continuous(breaks=seq(0,8), labels=parse(text=paste('10', seq(0,8), sep='^'))) | ||
| g.phred <- ggplot(df.phred.m <- melt(df.phred, id='readgroup'), aes(x=as.numeric(variable), y=pmax(log(value,10),0), group=readgroup, color=readgroup)) + geom_line() + theme_bw() + scale_x_continuous(limits=c(0,43)) + ylab('Reads') + xlab('Mean read Phred quality') + scale_y_continuous(breaks=seq(0,8), labels=parse(text=paste('10', seq(0,8), sep='^'))) | ||
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| pdf(opt$output, width=15, height=8) | ||
| print(grid.arrange(g.mapq, g.nm, g.isize, g.len, g.clip, g.phred, ncol=3)) | ||
| dev.off() | ||
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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