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0
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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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2
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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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3
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17 selection=${12}
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2
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18 outID="result"
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19
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20 echo "testID = $testID"
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21 echo "species = $species"
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22 echo "substitutionModel = $substitutionModel"
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23 echo "mutabilityModel = $mutabilityModel"
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24 echo "clonal = $clonal"
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25 echo "fixIndels = $fixIndels"
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26 echo "region = $region"
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27 echo "inputs = ${inputs[@]}"
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28 echo "IDs = ${IDs[@]}"
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29 echo "ref = $ref"
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30 echo "output = $output"
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31 echo "outID = $outID"
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32
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33 fasta="$PWD/baseline.fasta"
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34
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35
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36 count=0
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37 for current in ${inputs[@]}
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38 do
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39 f=$(file $current)
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40 zipType="Zip archive"
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41 if [[ "$f" == *"$zipType"* ]]
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42 then
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43 id=${IDs[$count]}
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44 echo "id=$id"
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45 unzip $current -d $PWD/$id/ >> $PWD/unziplog.log
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3
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46 summaryfile="$PWD/summary_${id}.txt"
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47 gappedfile="$PWD/gappednt_${id}.txt"
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48 filtered="$PWD/filtered_${id}.txt"
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49 cat $PWD/$id/*/1_* > $summaryfile
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50 cat $PWD/$id/*/2_* > $gappedfile
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51 Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered
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52
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53 final="$PWD/final_${id}.txt"
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54 cat $filtered | cut -f2,4,7 > $final
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55 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id
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2
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56 else
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57 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta
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58 fi
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59 count=$((count+1))
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60 done
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61 workdir="$PWD"
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62 cd $dir
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63 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1
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64
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65 echo "$workdir/${outID}.txt"
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66
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67 rows=`tail -n +2 $workdir/${outID}.txt | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '`
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68 rows=($rows)
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69 unset rows[${#rows[@]}-1]
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0
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70
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71 cd $dir
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2
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72 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1
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0
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73
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74
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2
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75
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0
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76
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2
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77
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