Mercurial > repos > davidvanzessen > baseline_bayesian_estimation
diff wrapper.sh @ 0:d685e7ba0ed4 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 15 Jul 2014 08:43:49 -0400 |
| parents | |
| children | e8dd8474aecb |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wrapper.sh Tue Jul 15 08:43:49 2014 -0400 @@ -0,0 +1,33 @@ +#!/bin/bash +dir="$(cd "$(dirname "$0")" && pwd)" + +testID=$1 +species=$2 +substitutionModel=$3 +mutabilityModel=$4 +clonal=$5 +fixIndels=$6 +region=$7 +input=$8 +outDir=$9 +#mkdir $outDir +outID=${10} +outFile=${11} +outFile2=${12} + +cd $dir +Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $input $dir/ $outID 2> /dev/null + +mv $dir/${outID}.txt $outFile +mv $dir/${outID}.RData $outFile2 + +#tail -n+2 $outDir/${outID}.txt > $outDir/tmp.txt +#echo "<html><table border='1'><thead>" >> $outFile +#echo "<tr><th>Type</th><th>ID</th><th>Observed_CDR_R</th><th>Observed_CDR_S</th><th>Observed_FWR_R</th><th>Observed_FWR_S</th><th>Expected_CDR_R</th><th>Expected_CDR_S</th><th>Expected_FWR_R</th><th>Expected_FWR_S</th><th>Focused_Sigma_CDR</th><th>Focused_CIlower_CDR</th><th>Focused_CIupper_CDR</th><th>Focused_Sigma_FWR</th><th>Focused_CIlower_FWR</th><th>Focused_CIupper_FWR</th><th>Focused_P_CDR</th><th>Focused_P_FWR</th></tr></thead><tbody>" >> $outFile +#while read Type ID Observed_CDR_R Observed_CDR_S Observed_FWR_R Observed_FWR_S Expected_CDR_R Expected_CDR_S Expected_FWR_R Expected_FWR_S Focused_Sigma_CDR Focused_CIlower_CDR Focused_CIupper_CDR Focused_Sigma_FWR Focused_CIlower_FWR Focused_CIupper_FWR Focused_P_CDR Focused_P_FWR +#do +# echo "<tr><td>$Type</td><td>$ID</td><td>$Observed_CDR_R</td><td>$Observed_CDR_S</td><td>$Observed_FWR_R</td><td>$Observed_FWR_S</td><td>$Expected_CDR_R</td><td>$Expected_CDR_S</td><td>$Expected_FWR_R</td><td>$Expected_FWR_S</td><td>$Focused_Sigma_CDR</td><td>$Focused_CIlower_CDR</td><td>$Focused_CIupper_CDR</td><td>$Focused_Sigma_FWR</td><td>$Focused_CIlower_FWR</td><td>$Focused_CIupper_FWR</td><td>$Focused_P_CDR</td><td>$Focused_P_FWR</td></tr>" >> $outFile +#done < $outDir/tmp.txt +#echo "</tbody></table></html>" >> $outFile +#rm $outDir/tmp.txt +