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comparison wrapper.sh @ 5:d8de51314d3f draft

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Uploaded
author davidvanzessen
date Thu, 14 Aug 2014 07:17:26 -0400
parents 38c038c17d0c
children 8a4183eed741
comparison
equal deleted inserted replaced
4:1726dc8f3e0a 5:d8de51314d3f
1
1 #!/bin/bash 2 #!/bin/bash
2 dir="$(cd "$(dirname "$0")" && pwd)" 3 dir="$(cd "$(dirname "$0")" && pwd)"
3 4
4 testID=$1 5 testID=$1
5 species=$2 6 species=$2
46 summaryfile="$PWD/summary_${id}.txt" 47 summaryfile="$PWD/summary_${id}.txt"
47 gappedfile="$PWD/gappednt_${id}.txt" 48 gappedfile="$PWD/gappednt_${id}.txt"
48 filtered="$PWD/filtered_${id}.txt" 49 filtered="$PWD/filtered_${id}.txt"
49 cat $PWD/$id/*/1_* > $summaryfile 50 cat $PWD/$id/*/1_* > $summaryfile
50 cat $PWD/$id/*/2_* > $gappedfile 51 cat $PWD/$id/*/2_* > $gappedfile
51 Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 52 Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 2>&1
52 53
53 final="$PWD/final_${id}.txt" 54 final="$PWD/final_${id}.txt"
54 cat $filtered | cut -f2,4,7 > $final 55 cat $filtered | cut -f2,4,7 > $final
55 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id 56 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id
56 else 57 else
62 cd $dir 63 cd $dir
63 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1 64 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1
64 65
65 echo "$workdir/${outID}.txt" 66 echo "$workdir/${outID}.txt"
66 67
67 rows=`tail -n +2 $workdir/${outID}.txt | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '` 68 rows=`tail -n +2 $workdir/${outID}.txt | grep -v "All sequences combined" | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '`
68 rows=($rows) 69 rows=($rows)
69 unset rows[${#rows[@]}-1] 70 #unset rows[${#rows[@]}-1]
70 71
71 cd $dir 72 cd $dir
72 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1 73 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1
73 74
74 75