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annotate baseline/wrapper.sh @ 0:64d74ba01a7c draft

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"planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
author rhpvorderman
date Wed, 27 Oct 2021 12:34:47 +0000
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1 #!/bin/bash
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2 dir="$(cd "$(dirname "$0")" && pwd)"
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3
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4 testID=$1
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5 species=$2
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6 substitutionModel=$3
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7 mutabilityModel=$4
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8 clonal=$5
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9 fixIndels=$6
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10 region=$7
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11 inputs=$8
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12 inputs=($inputs)
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13 IDs=$9
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14 IDs=($IDs)
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15 ref=${10}
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16 output=${11}
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17 selection=${12}
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18 output_table=${13}
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19 outID="result"
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20
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21 echo "$PWD"
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22
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23 echo "testID = $testID"
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24 echo "species = $species"
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25 echo "substitutionModel = $substitutionModel"
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26 echo "mutabilityModel = $mutabilityModel"
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27 echo "clonal = $clonal"
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28 echo "fixIndels = $fixIndels"
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29 echo "region = $region"
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30 echo "inputs = ${inputs[@]}"
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31 echo "IDs = ${IDs[@]}"
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32 echo "ref = $ref"
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33 echo "output = $output"
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34 echo "outID = $outID"
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35
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36 fasta="$PWD/baseline.fasta"
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37
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38
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39 count=0
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40 for current in ${inputs[@]}
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41 do
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42 f=$(file $current)
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43 zipType="Zip archive"
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44 if [[ "$f" == *"Zip archive"* ]] || [[ "$f" == *"XZ compressed data"* ]]
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45 then
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46 id=${IDs[$count]}
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47 echo "id=$id"
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48 if [[ "$f" == *"Zip archive"* ]] ; then
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49 echo "Zip archive"
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50 echo "unzip $input -d $PWD/files/"
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51 unzip $current -d "$PWD/$id/"
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52 elif [[ "$f" == *"XZ compressed data"* ]] ; then
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53 echo "ZX archive"
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54 echo "tar -xJf $input -C $PWD/files/"
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55 mkdir -p "$PWD/$id/files"
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56 tar -xJf $current -C "$PWD/$id/files/"
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57 fi
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58 filtered="$PWD/filtered_${id}.txt"
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59 imgt_1_file="`find $PWD/$id -name '1_*.txt'`"
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60 imgt_2_file="`find $PWD/$id -name '2_*.txt'`"
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61 echo "1_Summary file: ${imgt_1_file}"
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62 echo "2_IMGT-gapped file: ${imgt_2_file}"
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63 echo "filter.r for $id"
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64 Rscript $dir/filter.r ${imgt_1_file} ${imgt_2_file} "$selection" $filtered 2>&1
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65
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66 final="$PWD/final_${id}.txt"
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67 cat $filtered | cut -f2,4,7 > $final
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68 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id
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69 else
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70 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta
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71 fi
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72 count=$((count+1))
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73 done
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74 workdir="$PWD"
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75 cd $dir
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76 echo "file: ${inputs[0]}"
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77 #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1
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78 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1
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79
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80 echo "$workdir/${outID}.txt"
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81
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82 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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83 rows=($rows)
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84 #unset rows[${#rows[@]}-1]
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85
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86 cd $dir
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87 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1
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88 cp $workdir/result.txt ${output_table}
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