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Further, smarter modifications to R script for correctly accessing database data 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5124 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2011-01-29 03:32:20 +00:00
parent 4f2882c546
commit afeb0f63c3
1 changed files with 9 additions and 4 deletions
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13
R/DataProcessingReport/GetTearsheetStats.R
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@ -26,11 +26,12 @@ cmdargs = gsa.getargs(
bamlist = scan(cmdargs$bamlist, "character");
squids <- c()
print(paste("grep SQUID ", sub("cleaned.BamFiles.list", "yaml",cmdargs$bamlist) , ' |grep "C..." -o', sep=""))
squids <- system(paste("grep SQUID ", sub("cleaned.BamFiles.list", "yaml",cmdargs$bamlist) , ' |grep "C..." -o', sep=""), intern=TRUE)
fclanes = c();
for (bam in bamlist) {
bamheader = system(paste("samtools view -H", bam), intern=TRUE);
squids<-c(squids, strsplit(bam, "/")[[1]][4])
if (length(bamheader) > 0) {
rgs = bamheader[grep("^@RG", bamheader)];
@ -68,8 +69,11 @@ squid_fclanes = gsub("A.XX", "", squid_fclanes);
dproj = d[which(squid_fclanes %in% fclanes),];
dproj = dproj[which(dproj$"Project" %in% unique(squids)),]
d2proj = d2[which(d2$"Project" %in% unique(squids) & d2$"Sample" %in% dproj$"External ID"),];
d2proj = d2[which(d2$"Project" %in% unique(dproj$Project) & d2$"Sample" %in% dproj$"External ID"),];
tearsheet<-function(){
@ -231,7 +235,8 @@ tearsheet<-function(){
table3<-rbind(paste(instrument), used_lanes, sprintf("%s rejected by sequencing, %s by analysis\n", unused_lanes_by_sequencing, unused_lanes_by_analysis), sprintf("%0.1f +/- %0.1f lanes (median=%0.1f)\n", lanes_per_sample_mean, lanes_per_sample_sd, lanes_per_sample_median), sprintf("%s paired, %s widowed, %s single\n", lanes_paired, lanes_widowed, lanes_single), sprintf("%0.1f +/- %0.1f bases (median=%0.1f)\n", read_length_mean, read_length_sd, read_length_median), sprintf("\tSequencing dates: %s to %s\n", start_date, end_date))
print(nrow(table3))
print(table3)
rownames(table3)<-c("Sequencer", "Used lanes", "Unused lanes","Used lanes/sample", "Lane parities", "Read lengths", "Sequencing dates")
par(mar=c(0,0,1,0))