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5
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1
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0
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2 #!/bin/bash
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4
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5 testID=$1
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6 species=$2
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7 substitutionModel=$3
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8 mutabilityModel=$4
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9 clonal=$5
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10 fixIndels=$6
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11 region=$7
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2
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12 inputs=$8
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13 inputs=($inputs)
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14 IDs=$9
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15 IDs=($IDs)
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16 ref=${10}
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17 output=${11}
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3
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18 selection=${12}
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2
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19 outID="result"
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20
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21 echo "testID = $testID"
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22 echo "species = $species"
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23 echo "substitutionModel = $substitutionModel"
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24 echo "mutabilityModel = $mutabilityModel"
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25 echo "clonal = $clonal"
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26 echo "fixIndels = $fixIndels"
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27 echo "region = $region"
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28 echo "inputs = ${inputs[@]}"
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29 echo "IDs = ${IDs[@]}"
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30 echo "ref = $ref"
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31 echo "output = $output"
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32 echo "outID = $outID"
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33
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34 fasta="$PWD/baseline.fasta"
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35
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36
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37 count=0
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38 for current in ${inputs[@]}
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39 do
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40 f=$(file $current)
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41 zipType="Zip archive"
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42 if [[ "$f" == *"$zipType"* ]]
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43 then
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44 id=${IDs[$count]}
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45 echo "id=$id"
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46 unzip $current -d $PWD/$id/ >> $PWD/unziplog.log
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3
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47 summaryfile="$PWD/summary_${id}.txt"
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48 gappedfile="$PWD/gappednt_${id}.txt"
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49 filtered="$PWD/filtered_${id}.txt"
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6
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50 filecount=`ls -l $PWD/$id/ | wc -l`
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7
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51 if [[ "$filecount" -eq "2" ]]
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6
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52 then
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53 cat $PWD/$id/*/1_* > $summaryfile
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54 cat $PWD/$id/*/2_* > $gappedfile
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55 else
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56 cat $PWD/$id/1_* > $summaryfile
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57 cat $PWD/$id/2_* > $gappedfile
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58 fi
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5
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59 Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 2>&1
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3
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60
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61 final="$PWD/final_${id}.txt"
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62 cat $filtered | cut -f2,4,7 > $final
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63 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id
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2
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64 else
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65 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta
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66 fi
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67 count=$((count+1))
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68 done
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69 workdir="$PWD"
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70 cd $dir
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8
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71 echo "file: ${inputs[0]}"
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72 #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1
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2
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73 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1
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74
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75 echo "$workdir/${outID}.txt"
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76
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5
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77 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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2
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78 rows=($rows)
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5
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79 #unset rows[${#rows[@]}-1]
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0
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80
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81 cd $dir
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2
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82 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1
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0
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83
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84
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2
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85
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0
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86
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2
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87
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