Mercurial > repos > davidvanzessen > shm_csr
view baseline/wrapper.sh @ 32:4c5ba6b5d10d draft
Uploaded
author | davidvanzessen |
---|---|
date | Thu, 15 Dec 2016 09:21:54 -0500 |
parents | c33d93683a09 |
children | 8728284105ee |
line wrap: on
line source
#!/bin/bash dir="$(cd "$(dirname "$0")" && pwd)" testID=$1 species=$2 substitutionModel=$3 mutabilityModel=$4 clonal=$5 fixIndels=$6 region=$7 inputs=$8 inputs=($inputs) IDs=$9 IDs=($IDs) ref=${10} output=${11} selection=${12} output_table=${13} outID="result" echo "$PWD" 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" == *"$zipType"* ]] || [[ "$f" == *"XZ compressed data"* ]] then id=${IDs[$count]} echo "id=$id" if [[ "$f" == *"Zip archive"* ]] ; then echo "Zip archive" echo "unzip $input -d $PWD/files/" unzip $current -d "$PWD/$id/" elif [[ "$f" == *"XZ compressed data"* ]] ; then echo "ZX archive" echo "tar -xJf $input -C $PWD/files/" mkdir -p "$PWD/$id/files" tar -xJf $current -C "$PWD/$id/files/" fi summaryfile="$PWD/summary_${id}.txt" gappedfile="$PWD/gappednt_${id}.txt" filtered="$PWD/filtered_${id}.txt" filecount=`ls -l $PWD/$id/ | wc -l` if [[ "$filecount" -eq "2" ]] then cat $PWD/$id/*/1_* > $summaryfile cat $PWD/$id/*/2_* > $gappedfile else cat $PWD/$id/1_* > $summaryfile cat $PWD/$id/2_* > $gappedfile fi Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 2>&1 final="$PWD/final_${id}.txt" cat $filtered | cut -f2,4,7 > $final python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id else python $dir/script_xlsx.py --input $current --ref $ref --output $fasta fi count=$((count+1)) done if [[ $(wc -l < $fasta) -eq "1" ]]; then echo "No sequences in the fasta file, exiting" exit 0 fi workdir="$PWD" cd $dir echo "file: ${inputs[0]}" #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1 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 -v "All sequences combined" | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '` rows=($rows) #unset rows[${#rows[@]}-1] cd $dir Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1 cp $workdir/result.txt ${output_table}