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comparison baseline/wrapper.sh @ 4:5ffd52fc35c4 draft

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author davidvanzessen
date Mon, 12 Dec 2016 05:22:37 -0500
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3:beaa487ecf43 4:5ffd52fc35c4
1 #!/bin/bash
2 dir="$(cd "$(dirname "$0")" && pwd)"
3
4 testID=$1
5 species=$2
6 substitutionModel=$3
7 mutabilityModel=$4
8 clonal=$5
9 fixIndels=$6
10 region=$7
11 inputs=$8
12 inputs=($inputs)
13 IDs=$9
14 IDs=($IDs)
15 ref=${10}
16 output=${11}
17 selection=${12}
18 output_table=${13}
19 outID="result"
20
21 echo "$PWD"
22
23 echo "testID = $testID"
24 echo "species = $species"
25 echo "substitutionModel = $substitutionModel"
26 echo "mutabilityModel = $mutabilityModel"
27 echo "clonal = $clonal"
28 echo "fixIndels = $fixIndels"
29 echo "region = $region"
30 echo "inputs = ${inputs[@]}"
31 echo "IDs = ${IDs[@]}"
32 echo "ref = $ref"
33 echo "output = $output"
34 echo "outID = $outID"
35
36 fasta="$PWD/baseline.fasta"
37
38
39 count=0
40 for current in ${inputs[@]}
41 do
42 f=$(file $current)
43 zipType="Zip archive"
44 if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"XZ compressed data"* ]]
45 then
46 id=${IDs[$count]}
47 echo "id=$id"
48 if [[ "$f" == *"Zip archive"* ]] ; then
49 echo "Zip archive"
50 echo "unzip $input -d $PWD/files/"
51 unzip $current -d "$PWD/$id/"
52 elif [[ "$f" == *"XZ compressed data"* ]] ; then
53 echo "ZX archive"
54 echo "tar -xJf $input -C $PWD/files/"
55 mkdir -p "$PWD/$id/files"
56 tar -xJf $current -C "$PWD/$id/files/"
57 fi
58 summaryfile="$PWD/summary_${id}.txt"
59 gappedfile="$PWD/gappednt_${id}.txt"
60 filtered="$PWD/filtered_${id}.txt"
61 filecount=`ls -l $PWD/$id/ | wc -l`
62 if [[ "$filecount" -eq "2" ]]
63 then
64 cat $PWD/$id/*/1_* > $summaryfile
65 cat $PWD/$id/*/2_* > $gappedfile
66 else
67 cat $PWD/$id/1_* > $summaryfile
68 cat $PWD/$id/2_* > $gappedfile
69 fi
70 Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 2>&1
71
72 final="$PWD/final_${id}.txt"
73 cat $filtered | cut -f2,4,7 > $final
74 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id
75 else
76 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta
77 fi
78 count=$((count+1))
79 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"
87 cd $dir
88 echo "file: ${inputs[0]}"
89 #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/ $outID 2>&1
91
92 echo "$workdir/${outID}.txt"
93
94 rows=`tail -n +2 $workdir/${outID}.txt | grep -v "All sequences combined" | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '`
95 rows=($rows)
96 #unset rows[${#rows[@]}-1]
97
98 cd $dir
99 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1
100 cp $workdir/result.txt ${output_table}
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