Mercurial > repos > davidvanzessen > baseline_bayesian_estimation

comparison wrapper.sh @ 2:94fada165724 draft

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author davidvanzessen
date Wed, 13 Aug 2014 07:32:38 -0400
parents e8dd8474aecb
children 38c038c17d0c
comparison
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1:e8dd8474aecb 2:94fada165724
6 substitutionModel=$3 6 substitutionModel=$3
7 mutabilityModel=$4 7 mutabilityModel=$4
8 clonal=$5 8 clonal=$5
9 fixIndels=$6 9 fixIndels=$6
10 region=$7 10 region=$7
11 input=$8 11 inputs=$8
12 outDir=$9 12 inputs=($inputs)
13 #mkdir $outDir 13 IDs=$9
14 outID=${10} 14 IDs=($IDs)
15 outFile=${11} 15 ref=${10}
16 outFile2=${12} 16 output=${11}
17 outID="result"
18
19 echo "testID = $testID"
20 echo "species = $species"
21 echo "substitutionModel = $substitutionModel"
22 echo "mutabilityModel = $mutabilityModel"
23 echo "clonal = $clonal"
24 echo "fixIndels = $fixIndels"
25 echo "region = $region"
26 echo "inputs = ${inputs[@]}"
27 echo "IDs = ${IDs[@]}"
28 echo "ref = $ref"
29 echo "output = $output"
30 echo "outID = $outID"
31
32 fasta="$PWD/baseline.fasta"
33
34
35 count=0
36 for current in ${inputs[@]}
37 do
38 f=$(file $current)
39 zipType="Zip archive"
40 if [[ "$f" == *"$zipType"* ]]
41 then
42 id=${IDs[$count]}
43 echo "id=$id"
44 unzip $current -d $PWD/$id/ >> $PWD/unziplog.log
45 filename="$PWD/gappednt_${id}.txt"
46 cat $PWD/$id/*/2_* | cut -f2,4,7 > $filename
47 python $dir/script_imgt.py --input $filename --ref $ref --output $fasta --id $id
48 else
49 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta
50 fi
51 count=$((count+1))
52 done
53 workdir="$PWD"
54 cd $dir
55 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1
56
57 echo "$workdir/${outID}.txt"
58
59 rows=`tail -n +2 $workdir/${outID}.txt | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '`
60 rows=($rows)
61 unset rows[${#rows[@]}-1]
17 62
18 cd $dir 63 cd $dir
19 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $input $dir/ $outID 2>&1 64 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1
20 65
21 mv $dir/${outID}.txt $outFile
22 mv $dir/${outID}.RData $outFile2
23 66
24 #tail -n+2 $outDir/${outID}.txt > $outDir/tmp.txt
25 #echo "<html><table border='1'><thead>" >> $outFile
26 #echo "<tr><th>Type</th><th>ID</th><th>Observed_CDR_R</th><th>Observed_CDR_S</th><th>Observed_FWR_R</th><th>Observed_FWR_S</th><th>Expected_CDR_R</th><th>Expected_CDR_S</th><th>Expected_FWR_R</th><th>Expected_FWR_S</th><th>Focused_Sigma_CDR</th><th>Focused_CIlower_CDR</th><th>Focused_CIupper_CDR</th><th>Focused_Sigma_FWR</th><th>Focused_CIlower_FWR</th><th>Focused_CIupper_FWR</th><th>Focused_P_CDR</th><th>Focused_P_FWR</th></tr></thead><tbody>" >> $outFile
27 #while read Type ID Observed_CDR_R Observed_CDR_S Observed_FWR_R Observed_FWR_S Expected_CDR_R Expected_CDR_S Expected_FWR_R Expected_FWR_S Focused_Sigma_CDR Focused_CIlower_CDR Focused_CIupper_CDR Focused_Sigma_FWR Focused_CIlower_FWR Focused_CIupper_FWR Focused_P_CDR Focused_P_FWR
28 #do
29 # echo "<tr><td>$Type</td><td>$ID</td><td>$Observed_CDR_R</td><td>$Observed_CDR_S</td><td>$Observed_FWR_R</td><td>$Observed_FWR_S</td><td>$Expected_CDR_R</td><td>$Expected_CDR_S</td><td>$Expected_FWR_R</td><td>$Expected_FWR_S</td><td>$Focused_Sigma_CDR</td><td>$Focused_CIlower_CDR</td><td>$Focused_CIupper_CDR</td><td>$Focused_Sigma_FWR</td><td>$Focused_CIlower_FWR</td><td>$Focused_CIupper_FWR</td><td>$Focused_P_CDR</td><td>$Focused_P_FWR</td></tr>" >> $outFile
30 #done < $outDir/tmp.txt
31 #echo "</tbody></table></html>" >> $outFile
32 #rm $outDir/tmp.txt
33 67
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