Mercurial > repos > davidvanzessen > shm_csr
annotate baseline/wrapper.sh @ 98:d714f5ea83d7 draft default tip
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
| author | rhpvorderman |
|---|---|
| date | Wed, 10 Jan 2024 12:32:47 +0000 |
| parents | b6f9a640e098 |
| children |
| rev | line source |
|---|---|
| 81 | 1 #!/bin/bash |
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98
d714f5ea83d7
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents:
81
diff
changeset
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2 |
| 81 | 3 dir="$(cd "$(dirname "$0")" && pwd)" |
| 4 | |
| 5 testID=$1 | |
| 6 species=$2 | |
| 7 substitutionModel=$3 | |
| 8 mutabilityModel=$4 | |
| 9 clonal=$5 | |
| 10 fixIndels=$6 | |
| 11 region=$7 | |
| 12 inputs=$8 | |
| 13 inputs=($inputs) | |
| 14 IDs=$9 | |
| 15 IDs=($IDs) | |
| 16 ref=${10} | |
| 17 output=${11} | |
| 18 selection=${12} | |
| 19 output_table=${13} | |
| 20 outID="result" | |
| 21 | |
| 22 echo "$PWD" | |
| 23 | |
| 24 echo "testID = $testID" | |
| 25 echo "species = $species" | |
| 26 echo "substitutionModel = $substitutionModel" | |
| 27 echo "mutabilityModel = $mutabilityModel" | |
| 28 echo "clonal = $clonal" | |
| 29 echo "fixIndels = $fixIndels" | |
| 30 echo "region = $region" | |
| 31 echo "inputs = ${inputs[@]}" | |
| 32 echo "IDs = ${IDs[@]}" | |
| 33 echo "ref = $ref" | |
| 34 echo "output = $output" | |
| 35 echo "outID = $outID" | |
| 36 | |
| 37 fasta="$PWD/baseline.fasta" | |
| 38 | |
| 39 | |
| 40 count=0 | |
| 41 for current in ${inputs[@]} | |
| 42 do | |
| 43 f=$(file $current) | |
| 44 zipType="Zip archive" | |
| 45 if [[ "$f" == *"Zip archive"* ]] || [[ "$f" == *"XZ compressed data"* ]] | |
| 46 then | |
| 47 id=${IDs[$count]} | |
| 48 echo "id=$id" | |
| 49 if [[ "$f" == *"Zip archive"* ]] ; then | |
| 50 echo "Zip archive" | |
| 51 echo "unzip $input -d $PWD/files/" | |
| 52 unzip $current -d "$PWD/$id/" | |
| 53 elif [[ "$f" == *"XZ compressed data"* ]] ; then | |
| 54 echo "ZX archive" | |
| 55 echo "tar -xJf $input -C $PWD/files/" | |
| 56 mkdir -p "$PWD/$id/files" | |
| 57 tar -xJf $current -C "$PWD/$id/files/" | |
| 58 fi | |
| 59 filtered="$PWD/filtered_${id}.txt" | |
| 60 imgt_1_file="`find $PWD/$id -name '1_*.txt'`" | |
| 61 imgt_2_file="`find $PWD/$id -name '2_*.txt'`" | |
| 62 echo "1_Summary file: ${imgt_1_file}" | |
| 63 echo "2_IMGT-gapped file: ${imgt_2_file}" | |
| 64 echo "filter.r for $id" | |
| 65 Rscript $dir/filter.r ${imgt_1_file} ${imgt_2_file} "$selection" $filtered 2>&1 | |
| 66 | |
| 67 final="$PWD/final_${id}.txt" | |
| 68 cat $filtered | cut -f2,4,7 > $final | |
| 69 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id | |
| 70 else | |
| 71 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta | |
| 72 fi | |
| 73 count=$((count+1)) | |
| 74 done | |
| 75 workdir="$PWD" | |
| 76 cd $dir | |
| 77 echo "file: ${inputs[0]}" | |
| 78 #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1 | |
| 79 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1 | |
| 80 | |
| 81 echo "$workdir/${outID}.txt" | |
| 82 | |
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98
d714f5ea83d7
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents:
81
diff
changeset
|
83 if [[ -f "$workdir/${outID}.txt" ]] |
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d714f5ea83d7
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents:
81
diff
changeset
|
84 then |
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d714f5ea83d7
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents:
81
diff
changeset
|
85 rows=`tail -n +2 $workdir/${outID}.txt | grep -v "All sequences combined" | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '` |
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d714f5ea83d7
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents:
81
diff
changeset
|
86 rows=($rows) |
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d714f5ea83d7
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents:
81
diff
changeset
|
87 #unset rows[${#rows[@]}-1] |
| 81 | 88 |
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98
d714f5ea83d7
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents:
81
diff
changeset
|
89 cd $dir |
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d714f5ea83d7
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents:
81
diff
changeset
|
90 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1 |
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d714f5ea83d7
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents:
81
diff
changeset
|
91 cp $workdir/result.txt ${output_table} |
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d714f5ea83d7
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
rhpvorderman
parents:
81
diff
changeset
|
92 fi |
| 81 | 93 |
| 94 | |
| 95 |