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1 #!/bin/bash
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2
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1
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3 mkdir $PWD/igblastdatabase
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4 unzip $dir/database.zip -d $PWD/igblastdatabase/
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5
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6 export IGDATA=$PWD/igblastdatabase/
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0
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7
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8 clonalType=${@:(-3):1}
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9 html=${@:(-2):1}
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10 imageDir=${@:(-1):1}
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11 dataCount=`expr $# - 3`
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12 inputData=${@:(1):dataCount}
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13 dir="$(cd "$(dirname "$0")" && pwd)"
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14 array=("$@")
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15 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
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16 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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17
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1
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18
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19
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0
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20 function blastAndParse {
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21 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html
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22 echo "$IGDATA/bin/igblastn -germline_db_V $IGDATA/database/human_gl_V -germline_db_J $IGDATA/database/human_gl_J -germline_db_D $IGDATA/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4"
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2
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23 igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4
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0
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24 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
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25
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26 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html
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27 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > $5
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28 echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html
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29 }
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30
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31 id=${inputData[0]}
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32 forwardSlash="/"
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33 mergerInput=()
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34 count=0
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35 for current in $inputData; do
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36 if [[ "$current" != *"$forwardSlash"* ]]; then
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37 id=$current
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38 count=0
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39 mergerInput+=($id)
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40 continue
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41 fi
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42 fileName=$(basename $current)
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43 parsedFileName="${fileName%.*}"
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44 parsedFileName="$PWD/$parsedFileName.parsed"
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45 blastAndParse $current $id $count $fileName $parsedFileName &
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46 mergerInput+=($parsedFileName)
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47 count=$((count+1))
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48 done
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49 wait
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50
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51
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52
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53 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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54 echo "<tr><td>merging</td></tr>" >> $html
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55
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56 python $dir/igblastmerge.py ${mergerInput[*]} --output $PWD/merged.txt
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57
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58 echo "<tr><td>done</td></tr>" >> $html
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59 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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60 echo "<tr><td>plotting</td></tr>" >> $html
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61
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62
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63 inputFile=$PWD/merged.txt
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64 outputFile=$html
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65 outputDir=$imageDir
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66 mkdir $outputDir
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67 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
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68 echo "<html>" > $outputFile
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69 echo "<img src='VPlot.png'/>" >> $outputFile
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70 echo "<img src='DPlot.png'/>" >> $outputFile
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71 echo "<img src='JPlot.png'/>" >> $outputFile
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72
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73 samples=`cat $outputDir/samples.txt`
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74 count=1
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75 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
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76 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
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77 for sample in $samples; do
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78 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
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79 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
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80 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
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81
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82 echo "$hasReplicateColumn"
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83 #if its a 'new' merged file with replicate info
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84 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
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85 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
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86
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87 #replicate,reads,squared
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88 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
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89 while IFS=, read replicate reads squared
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90 do
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91
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92 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
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93 done < $outputDir/ReplicateReads_$sample.csv
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94
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95 #sum of reads and reads squared
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96 while IFS=, read readsSum squaredSum
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97 do
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98 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
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99 done < $outputDir/ReplicateSumReads_$sample.csv
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100
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101 echo "</table></td></tr>" >> $outputFile
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102
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103 #overview
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104 echo "<tr><td colspan='3'><table border='1'><tr><th>Coincidence Type</th><th>Raw Coincidence Freq</th><th>Coincidence Weight</th><th>Coincidences, Weighted</th></tr>" >> $outputFile
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105 while IFS=, read type count weight weightedCount
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106 do
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107 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
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108 done < $outputDir/ClonalityOverView_$sample.csv
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109 echo "</table></td></tr>" >> $outputFile
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110 fi
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111
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112 echo "<tr><td><h2>V-D Heatmap:</h2></td><td><h2>V-J Heatmap:</h2></td><td><h2>D-J Heatmap:</h2></td></tr><tr>" >> $outputFile
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113 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
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114 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
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115 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
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116 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
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117 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
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118 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
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119 count=$((count+1))
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120 done
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121 echo "</table>" >> $outputFile
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122
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123 echo "</html>" >> $outputFile
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