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"Properly handles multiplexed and non multiplex lane data from the picard database." 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5146 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2011-01-31 21:14:32 +00:00
parent 4cb910bc38
commit 1753f9d864
1 changed files with 21 additions and 11 deletions
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30
R/DataProcessingReport/GetTearsheetStats.R
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@ -29,7 +29,8 @@ cmdargs = gsa.getargs(
bamlist = scan(cmdargs$bamlist, "character"); bamlist = scan(cmdargs$bamlist, "character");
print(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o', sep="")) print(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o', sep=""))
squids <- system(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o', sep=""), intern=TRUE) squids <- system(paste("grep SQUID ", cmdargs$yaml, ' |grep "C..." -o', sep=""), intern=TRUE)
fclanes = c(); indexed = c();
nonindexed = c();
for (bam in bamlist) { for (bam in bamlist) {
bamheader = system(paste("samtools view -H", bam), intern=TRUE); bamheader = system(paste("samtools view -H", bam), intern=TRUE);
@ -40,13 +41,21 @@ for (bam in bamlist) {
for (rg in rgs) { for (rg in rgs) {
id = grep("PU:", unlist(strsplit(rg, "\t")), value=TRUE); id = grep("PU:", unlist(strsplit(rg, "\t")), value=TRUE);
id = sub("PU:", "", id); id = sub("PU:", "", id);
id = gsub("A.XX......", "", id) id = gsub("XX......", "XX", id)
##change this so that it pulls out the flowcell and lane properly from old samples if (length(unlist(strsplit(id, "\\.")))==3){
##change this so that it pulls out only samples which are in the right project for new samples indexed<-c(indexed, id)
fclanes = c(fclanes, id); }
else{
if(length(unlist(strsplit(id, "\\.")))==2){
nonindexed<-c(nonindexed, id)
}
else{
print(id + " is a strange PU and will result in odd searches")
}
}
} }
} else { } else {
Print(sprintf("Could not load '%s'\n", bam)); print(sprintf("Could not load '%s'\n", bam));
} }
} }
@ -66,10 +75,11 @@ dbClearResult(rs2);
oraCloseDriver(drv); oraCloseDriver(drv);
squid_fclanes = sprintf("%s.%s", d$"Flowcell", d$"Lane"); squid_fclanes = sprintf("%s.%s", d$"Flowcell", d$"Lane");
squid_fclanes = gsub("A.XX", "", squid_fclanes); squid_fclanes_indexed = sprintf("%s.%s.%s", d$"Flowcell", d$"Lane", d$"Barcode");
dproj = d[which(squid_fclanes %in% fclanes),]; dproj = d[which(squid_fclanes %in% nonindexed),];
dproj = rbind(dproj, d[which(squid_fclanes_indexed %in% indexed),])
dproj = dproj[which(dproj$"Project" %in% unique(squids)),] dproj = dproj[which(dproj$"Project" %in% unique(squids)),]
@ -295,13 +305,13 @@ tearsheet<-function(){
par(mar=c(5, 4, 4, 2) + 0.1) par(mar=c(5, 4, 4, 2) + 0.1)
ind = order(eval.bysample.called.all$CountVariants); ind = order(eval.bysample.called.all$CountVariants);
plot(c(1:length(eval.bysample.called.all$CountVariants)), eval.bysample.called.all$CountVariants[ind], col="black", cex=1.1, cex.lab=1.1, cex.axis=1.1, main="Varients per Sample", xlab="Sample", ylab="Number of variants", bty="n", ylim=c(0, max(eval.bysample.called.all$CountVariants))); plot(c(1:length(eval.bysample.called.all$CountVariants)), eval.bysample.called.all$CountVariants[ind], col="black", cex=1.1, cex.lab=1.1, cex.axis=1.1, main="Variants per Sample", xlab="Sample", ylab="Number of variants", bty="n", ylim=c(0, max(eval.bysample.called.all$CountVariants)));
points(c(1:length(eval.bysample.called.known$CountVariants)), eval.bysample.called.known$CountVariants[ind], col="blue", cex=1.3); points(c(1:length(eval.bysample.called.known$CountVariants)), eval.bysample.called.known$CountVariants[ind], col="blue", cex=1.3);
points(c(1:length(eval.bysample.called.novel$CountVariants)), eval.bysample.called.novel$CountVariants[ind], col="red", cex=1.3); points(c(1:length(eval.bysample.called.novel$CountVariants)), eval.bysample.called.novel$CountVariants[ind], col="red", cex=1.3);
legend("right", max(eval.bysample.called.all$CountVariants)/2, c("All", "Known", "Novel"), col=c("black", "blue", "red"), pt.cex=1.3, pch=21); legend("right", max(eval.bysample.called.all$CountVariants)/2, c("All", "Known", "Novel"), col=c("black", "blue", "red"), pt.cex=1.3, pch=21);
par(mar=c(5, 4, 4, 2) + 0.1) par(mar=c(5, 4, 4, 2) + 0.1)
plot(eval.ac.called.all$AC, eval.ac.called.all$n, col="black", type="l", lwd=2, cex=1.1, cex.lab=1.1, cex.axis=1.1, xlab="Allele count", ylab="Number of variants", main="Varients by Allele Count", log="xy", bty="n"); plot(eval.ac.called.all$AC, eval.ac.called.all$n, col="black", type="l", lwd=2, cex=1.1, cex.lab=1.1, cex.axis=1.1, xlab="Allele count", ylab="Number of variants", main="Variants by Allele Count", log="xy", bty="n");
points(eval.ac.called.known$AC, eval.ac.called.known$n, col="blue", type="l", lwd=2); points(eval.ac.called.known$AC, eval.ac.called.known$n, col="blue", type="l", lwd=2);
points(eval.ac.called.novel$AC, eval.ac.called.novel$n, col="red", type="l", lwd=2); points(eval.ac.called.novel$AC, eval.ac.called.novel$n, col="red", type="l", lwd=2);
legend("topright", c("All", "Known", "Novel"), col=c("black", "blue", "red"), lwd=2); legend("topright", c("All", "Known", "Novel"), col=c("black", "blue", "red"), lwd=2);