Mercurial > repos > geert-vandeweyer > dc_genotyper
changeset 19:8938f339ed37 draft
Added output of pdf report with distributions
| author | geert-vandeweyer |
|---|---|
| date | Mon, 29 Sep 2014 05:19:48 -0400 |
| parents | 93f4d7524823 |
| children | 8262299f8f3c |
| files | DC_Genotyper.pl DC_Genotyper.xml |
| diffstat | 2 files changed, 16 insertions(+), 16 deletions(-) [+] |
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--- a/DC_Genotyper.pl Mon Sep 29 04:00:18 2014 -0400 +++ b/DC_Genotyper.pl Mon Sep 29 05:19:48 2014 -0400 @@ -298,20 +298,20 @@ print OUT "par(mfrow=c(2, 2))\n"; print OUT "for (i in 1:nrow(dists)) {\n"; print OUT " if (dists[i,'avg'] > 0.5) {\n"; -print OUT " x <- seq(0.85,1,length=1000))\n"; -print OUT " y <- dnorm(x,mean=dists[i,'avg'],sd=dists[i,'sd']))\n"; -print OUT " plot(x,y,main=paste('Distribution for allele \"',dists[i,'allele'],'\"',sep=''),xlab='Allelic Ratio',type='l',lwd=1))\n"; -print OUT " abline(v=(dists[i,'avg']-3*dists[i,'sd']),col='red'))\n"; -print OUT " text(0.855,max(y-0.5),paste(c('avg: ',round(dists[i,'avg'],digits=5),'\\nsd: ',round(dists[i,'sd'],digits=5),'\\nN: ',dists[i,'N']),sep=' ',collapse=''),adj=c(0,1)))\n"; -print OUT " } else {)\n"; -print OUT " x <- seq(0,0.15,length=1000))\n"; -print OUT " y <- dnorm(x,dists[i,'avg'],sd=dists[i,'sd']))\n"; -print OUT " plot(x,y,main=paste('Distribution for \"',dists[i,'allele'],'\" variation',sep=''),xlab='Allelic Ratio',type='l',lwd=1))\n"; -print OUT " abline(v=(dists[i,'avg']+3*dists[i,'sd']),col='red'))\n"; -print OUT " text(0.1,max(y-0.5),paste(c('avg: ',round(dists[i,'avg'],digits=5),'\\nsd: ',round(dists[i,'sd'],digits=5),'\\nN: ',dists[i,'N']),sep=' ',collapse=''),adj=c(0,1)))\n"; -print OUT " })\n"; -print OUT "})\n"; -print OUT "dev.off())\n"; +print OUT " x <- seq(0.85,1,length=1000)\n"; +print OUT " y <- dnorm(x,mean=dists[i,'avg'],sd=dists[i,'sd'])\n"; +print OUT " plot(x,y,main=paste('Distribution for allele \"',dists[i,'allele'],'\"',sep=''),xlab='Allelic Ratio',type='l',lwd=1)\n"; +print OUT " abline(v=(dists[i,'avg']-3*dists[i,'sd']),col='red')\n"; +print OUT " text(0.855,max(y-0.5),paste(c('avg: ',round(dists[i,'avg'],digits=5),'\\nsd: ',round(dists[i,'sd'],digits=5),'\\nN: ',dists[i,'N']),sep=' ',collapse=''),adj=c(0,1))\n"; +print OUT " } else {\n"; +print OUT " x <- seq(0,0.15,length=1000)\n"; +print OUT " y <- dnorm(x,dists[i,'avg'],sd=dists[i,'sd'])\n"; +print OUT " plot(x,y,main=paste('Distribution for \"',dists[i,'allele'],'\" variation',sep=''),xlab='Allelic Ratio',type='l',lwd=1)\n"; +print OUT " abline(v=(dists[i,'avg']+3*dists[i,'sd']),col='red')\n"; +print OUT " text(0.1,max(y-0.5),paste(c('avg: ',round(dists[i,'avg'],digits=5),'\\nsd: ',round(dists[i,'sd'],digits=5),'\\nN: ',dists[i,'N']),sep=' ',collapse=''),adj=c(0,1))\n"; +print OUT " }\n"; +print OUT "}\n"; +print OUT "dev.off()\n"; close OUT; system("cd $wd && Rscript MakePlots.R > /dev/null 2>&1"); @@ -474,7 +474,7 @@ } ## get counts. my $target = "$chr:$start-$stop"; - my $command = "igvtools count -w 1 --bases --query '$target' '$bam' '$wd/WIGS/$chr-$start-$stop.wig' '$igvgenome' > /dev/null 2>&1"; + my $command = "igvtools count -w 1 --bases --query '$target' '$wd/input.bam' '$wd/WIGS/$chr-$start-$stop.wig' '$igvgenome' > /dev/null 2>&1"; system($command); open WIG, "$wd/WIGS/$chr-$start-$stop.wig"; my $h = <WIG>;
--- a/DC_Genotyper.xml Mon Sep 29 04:00:18 2014 -0400 +++ b/DC_Genotyper.xml Mon Sep 29 05:19:48 2014 -0400 @@ -60,7 +60,7 @@ <outputs> <data format='txt' name="output1" label="${tool.name} on ${on_string}: Allele Fraction Distributions (TXT)"/> - <data format='pdf' name="output3" lable="${tool.name} on ${on_string}: Allele Fraction Distributions (PDF)"/> + <data format='pdf' name="output3" label="${tool.name} on ${on_string}: Allele Fraction Distributions (PDF)"/> <data format='vcf' name='output2' label="${tool.name} on ${on_string}: VCF file" /> </outputs> <help>