Mercurial > repos > davidvanzessen > baseline_bayesian_estimation
diff wrapper.sh @ 2:94fada165724 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 13 Aug 2014 07:32:38 -0400 |
| parents | e8dd8474aecb |
| children | 38c038c17d0c |
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--- a/wrapper.sh Tue Jul 15 09:00:24 2014 -0400 +++ b/wrapper.sh Wed Aug 13 07:32:38 2014 -0400 @@ -8,26 +8,62 @@ clonal=$5 fixIndels=$6 region=$7 -input=$8 -outDir=$9 -#mkdir $outDir -outID=${10} -outFile=${11} -outFile2=${12} +inputs=$8 +inputs=($inputs) +IDs=$9 +IDs=($IDs) +ref=${10} +output=${11} +outID="result" + +echo "testID = $testID" +echo "species = $species" +echo "substitutionModel = $substitutionModel" +echo "mutabilityModel = $mutabilityModel" +echo "clonal = $clonal" +echo "fixIndels = $fixIndels" +echo "region = $region" +echo "inputs = ${inputs[@]}" +echo "IDs = ${IDs[@]}" +echo "ref = $ref" +echo "output = $output" +echo "outID = $outID" + +fasta="$PWD/baseline.fasta" + + +count=0 +for current in ${inputs[@]} +do + f=$(file $current) + zipType="Zip archive" + if [[ "$f" == *"$zipType"* ]] + then + id=${IDs[$count]} + echo "id=$id" + unzip $current -d $PWD/$id/ >> $PWD/unziplog.log + filename="$PWD/gappednt_${id}.txt" + cat $PWD/$id/*/2_* | cut -f2,4,7 > $filename + python $dir/script_imgt.py --input $filename --ref $ref --output $fasta --id $id + else + python $dir/script_xlsx.py --input $current --ref $ref --output $fasta + fi + count=$((count+1)) +done +workdir="$PWD" +cd $dir +Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1 + +echo "$workdir/${outID}.txt" + +rows=`tail -n +2 $workdir/${outID}.txt | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '` +rows=($rows) +unset rows[${#rows[@]}-1] cd $dir -Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $input $dir/ $outID 2>&1 +Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1 -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 + +