/usr/bin/fastx-graph is in ea-utils 1.1.2+dfsg-4build1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 | #!/usr/bin/Rscript --vanilla
# Copyright (c) 2011 Expression Analysis / Gunjan Hariani, Erik Aronesty
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# $Id: fastx-graph 525 2012-12-25 19:41:22Z earonesty $
if (!require(getopt)) {
write(c("Installing package on:",system("hostname",intern=T)),file=stderr())
install.packages('getopt',repos='http://R-Forge.R-project.org')
# will die if it fails at this point
library(getopt)
}
if (!require("Hmisc")) {
write(c("Installing package on:",system("hostname",intern=T)),file=stderr())
install.packages('Hmisc',repos='http://R-Forge.R-project.org')
# will die if it fails at this point
library("Hmisc")
}
spec <- matrix(c(
'input' , 'i', 1, "character", "file from fastq-stats -x (required)",
'gc' , 'G', 1, "character", "input gc content file (optional)",
'out' , 'o', 1, "character", "output filename (optional)",
'help' , 'h', 0, "logical", "this help"
),ncol=5,byrow=T)
opt = getopt(spec);
if (!is.null(opt$help) || is.null(opt$input)) {
cat(paste(getopt(spec, usage=T, command="fastx-graph"),"\n"));
q();
}
in.file <- opt$input
gc.file <- opt$gc
out.file <- opt$out
fastx <- read.table(in.file,sep="\t",header=T,as.is=T)
# output is in, minus txt, plus png
if (is.null(out.file)) {
in.file <- gsub(".txt$","",in.file,perl=T)
out.file <- paste(in.file,".png",sep="")
}
# correct for bug in R if the file has a % sign in it
out.file <- gsub("%","%%",out.file)
png(out.file,width=1000, height=500)
par(mar=c(4,3,5,5),xaxs="i",yaxs="i",xpd=T)
plot(c(0,0),pch="",ylim=c(min(c(0,fastx$lW)),max(41,fastx$rW)),xlim=c(0,(nrow(fastx)+1)),
xlab="",ylab="",las=2,cex.axis=.85,cex.lab=.85,xaxt="n")
lims <- par("xaxp")[1:2]
major.ticks <- pretty(lims,n=par("xaxp")[3])
minor.tick(nx=(major.ticks[2]-major.ticks[1]),ny=10)
minor.ticks <- 1:nrow(fastx)
mtext("Cycle",side=3,line=3,cex=.85)
axis(1,at=major.ticks,cex.axis=.85,labels=F)
axis(3,at=major.ticks,cex.axis=.85,labels=F)
axis(3,at=minor.ticks,tcl=par("tcl")*0.5,labels=minor.ticks,cex.axis=.80,las=3)
colnames(fastx) <- c("column","count","min","max","sum","mean","Q1","med",
"Q3","IQR","lW","rW","A_count","C_count","G_count",
"T_count","N_count","Max_count")
for(i in 1:nrow(fastx)) {
par(new=T)
rect(fastx$column[i]-.35,fastx$Q1[i],fastx$column[i]+0.35,fastx$Q3[i],col="gray")
segments(fastx$column[i]-.35,fastx$med[i],fastx$column[i]+0.35,fastx$med[i],col="red",lwd=1.5)
segments(fastx$column[i],fastx$lW[i],fastx$column[i],fastx$Q1[i],lty="dashed")
segments(fastx$column[i],fastx$Q3[i],fastx$column[i],fastx$rW[i],lty="dashed")
segments(fastx$column[i]-.35,fastx$lW[i],fastx$column[i]+0.35,fastx$lW[i])
segments(fastx$column[i]-.35,fastx$rW[i],fastx$column[i]+0.35,fastx$rW[i])
}
# if theres a significant difference
tots<-fastx$N_count+fastx$T_count+fastx$G_count+fastx$C_count+fastx$A_count
if (min(tots) < (max(tots)*.98)) {
par(new=T)
plot(tots,col="gray",xaxt="n",yaxt="n",xlab="",ylab="",pch="+",ylim=c(min(tots),max(tots)))
lines(fastx$N_count+fastx$T_count+fastx$G_count+fastx$C_count+fastx$A_count,col="gray",xaxt="n",yaxt="n",xlab="",ylab="", lty=2)
}
par(new=T)
plot(fastx$column,fastx$A_count*100/fastx$count,col="red",type="l",xaxt="n",yaxt="n",xlab="",ylab="",
ylim=c(0,100),lwd=2)
par(new=T)
plot(fastx$column,fastx$C_count*100/fastx$count,col="blue",type="l",xaxt="n",yaxt="n",xlab="",ylab="",
ylim=c(0,100),lwd=2)
par(new=T)
plot(fastx$column,fastx$G_count*100/fastx$count,col="green",type="l",xaxt="n",yaxt="n",xlab="",ylab="",
ylim=c(0,100),lwd=2)
par(new=T)
plot(fastx$column,fastx$T_count*100/fastx$count,col="black",type="l",xaxt="n",yaxt="n",xlab="",ylab="",
ylim=c(0,100),lwd=2)
par(new=T)
barplot(fastx$N_count*100/fastx$count,col="orange",xaxt="n",yaxt="n",xlab="",ylab="",
ylim=c(0,100))
axis(4,at=seq(0,100,25),cex.axis=.85)
mtext("Pct Base Distribution",side=4,line=3,cex=.85)
mtext("Base Quality",side=2,line=2,cex=.85)
legend(0,-4,col=c("red","blue","green","black","orange"),lty=1,
legend=c("A","C","G","T","N"),cex=.70,horiz=T,lwd=2)
if(!is.null(gc.file)) {
tmp <- read.table(gc.file,sep="\t",header=F,as.is=T)
if (tmp[1,1] == 'pct-GC') {
# silly legacy format
GC <- read.table(gc.file,sep="\t",header=T,as.is=T,skip=3)
} else if (tmp[1,1] == 'pct_GC') {
GC <- read.table(gc.file,sep="\t",header=T,as.is=T,skip=1)
} else {
GC <- read.table(gc.file,sep="\t",header=T,as.is=T)
}
colnames(GC)=c("pct_gc", "count")
par(new=T)
par(fig=c(0.1,0.2,0.45,0.60))
par(mar=c(0,0,1,0))
plot(GC$pct_gc,GC$count,type="l",xaxt="n",yaxt="n",
main="%GC per read",cex.main=.90)
axis(1,seq(0,100,20),labels=seq(0,100,20),las=2,tck=-0.1,cex.axis=.75)
}
graphics.off()
|