Mercurial > repos > davidvanzessen > shm_csr
comparison baseline/wrapper.sh @ 63:8728284105ee draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 06 Dec 2017 08:04:52 -0500 |
| parents | c33d93683a09 |
| children |
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| 62:aa8d37bd1930 | 63:8728284105ee |
|---|---|
| 39 count=0 | 39 count=0 |
| 40 for current in ${inputs[@]} | 40 for current in ${inputs[@]} |
| 41 do | 41 do |
| 42 f=$(file $current) | 42 f=$(file $current) |
| 43 zipType="Zip archive" | 43 zipType="Zip archive" |
| 44 if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"XZ compressed data"* ]] | 44 if [[ "$f" == *"Zip archive"* ]] || [[ "$f" == *"XZ compressed data"* ]] |
| 45 then | 45 then |
| 46 id=${IDs[$count]} | 46 id=${IDs[$count]} |
| 47 echo "id=$id" | 47 echo "id=$id" |
| 48 if [[ "$f" == *"Zip archive"* ]] ; then | 48 if [[ "$f" == *"Zip archive"* ]] ; then |
| 49 echo "Zip archive" | 49 echo "Zip archive" |
| 53 echo "ZX archive" | 53 echo "ZX archive" |
| 54 echo "tar -xJf $input -C $PWD/files/" | 54 echo "tar -xJf $input -C $PWD/files/" |
| 55 mkdir -p "$PWD/$id/files" | 55 mkdir -p "$PWD/$id/files" |
| 56 tar -xJf $current -C "$PWD/$id/files/" | 56 tar -xJf $current -C "$PWD/$id/files/" |
| 57 fi | 57 fi |
| 58 summaryfile="$PWD/summary_${id}.txt" | |
| 59 gappedfile="$PWD/gappednt_${id}.txt" | |
| 60 filtered="$PWD/filtered_${id}.txt" | 58 filtered="$PWD/filtered_${id}.txt" |
| 61 filecount=`ls -l $PWD/$id/ | wc -l` | 59 imgt_1_file="`find $PWD/$id -name '1_*.txt'`" |
| 62 if [[ "$filecount" -eq "2" ]] | 60 imgt_2_file="`find $PWD/$id -name '2_*.txt'`" |
| 63 then | 61 echo "1_Summary file: ${imgt_1_file}" |
| 64 cat $PWD/$id/*/1_* > $summaryfile | 62 echo "2_IMGT-gapped file: ${imgt_2_file}" |
| 65 cat $PWD/$id/*/2_* > $gappedfile | 63 echo "filter.r for $id" |
| 66 else | 64 Rscript $dir/filter.r ${imgt_1_file} ${imgt_2_file} "$selection" $filtered 2>&1 |
| 67 cat $PWD/$id/1_* > $summaryfile | |
| 68 cat $PWD/$id/2_* > $gappedfile | |
| 69 fi | |
| 70 Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 2>&1 | |
| 71 | 65 |
| 72 final="$PWD/final_${id}.txt" | 66 final="$PWD/final_${id}.txt" |
| 73 cat $filtered | cut -f2,4,7 > $final | 67 cat $filtered | cut -f2,4,7 > $final |
| 74 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id | 68 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id |
| 75 else | 69 else |
| 76 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta | 70 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta |
| 77 fi | 71 fi |
| 78 count=$((count+1)) | 72 count=$((count+1)) |
| 79 done | 73 done |
| 80 | |
| 81 if [[ $(wc -l < $fasta) -eq "1" ]]; then | |
| 82 echo "No sequences in the fasta file, exiting" | |
| 83 exit 0 | |
| 84 fi | |
| 85 | |
| 86 workdir="$PWD" | 74 workdir="$PWD" |
| 87 cd $dir | 75 cd $dir |
| 88 echo "file: ${inputs[0]}" | 76 echo "file: ${inputs[0]}" |
| 89 #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1 | 77 #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1 |
| 90 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1 | 78 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1 |