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1 #!/bin/bash
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2
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3 #export IGDATA=/home/david/tmp/ncbi-igblast-1.0.0;
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4
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5 clonalType=${@:(-3):1}
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6 html=${@:(-2):1}
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7 imageDir=${@:(-1):1}
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8 dataCount=`expr $# - 3`
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9 inputData=${@:(1):dataCount}
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10 dir="$(cd "$(dirname "$0")" && pwd)"
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11 array=("$@")
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12 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
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13 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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14
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15 function blastAndParse {
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16 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html
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17 echo "$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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18 $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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19 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
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20
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21 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html
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22 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > $5
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23 echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html
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24 }
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25
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26 id=${inputData[0]}
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27 forwardSlash="/"
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28 mergerInput=()
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29 count=0
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30 for current in $inputData; do
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31 if [[ "$current" != *"$forwardSlash"* ]]; then
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32 id=$current
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33 count=0
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34 mergerInput+=($id)
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35 continue
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36 fi
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37 fileName=$(basename $current)
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38 parsedFileName="${fileName%.*}"
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39 parsedFileName="$PWD/$parsedFileName.parsed"
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40 blastAndParse $current $id $count $fileName $parsedFileName &
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41 mergerInput+=($parsedFileName)
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42 count=$((count+1))
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43 done
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44 wait
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45
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46
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47
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48 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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49 echo "<tr><td>merging</td></tr>" >> $html
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50
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51 python $dir/igblastmerge.py ${mergerInput[*]} --output $PWD/merged.txt
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52
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53 echo "<tr><td>done</td></tr>" >> $html
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54 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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55 echo "<tr><td>plotting</td></tr>" >> $html
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56
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57
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58 inputFile=$PWD/merged.txt
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59 outputFile=$html
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60 outputDir=$imageDir
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61 mkdir $outputDir
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62 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
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63 echo "<html>" > $outputFile
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64 echo "<img src='VPlot.png'/>" >> $outputFile
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65 echo "<img src='DPlot.png'/>" >> $outputFile
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66 echo "<img src='JPlot.png'/>" >> $outputFile
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67
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68 samples=`cat $outputDir/samples.txt`
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69 count=1
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70 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
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71 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
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72 for sample in $samples; do
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73 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
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74 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
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75 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
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76
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77 echo "$hasReplicateColumn"
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78 #if its a 'new' merged file with replicate info
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79 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
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80 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
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81
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82 #replicate,reads,squared
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83 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
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84 while IFS=, read replicate reads squared
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85 do
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86
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87 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
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88 done < $outputDir/ReplicateReads_$sample.csv
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89
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90 #sum of reads and reads squared
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91 while IFS=, read readsSum squaredSum
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92 do
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93 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
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94 done < $outputDir/ReplicateSumReads_$sample.csv
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95
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96 echo "</table></td></tr>" >> $outputFile
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97
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98 #overview
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99 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>" >> $outputFile
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100 while IFS=, read type count weight weightedCount
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101 do
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102 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
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103 done < $outputDir/ClonalityOverView_$sample.csv
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104 echo "</table></td></tr>" >> $outputFile
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105 fi
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106
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107 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>" >> $outputFile
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108 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
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109 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
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110 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
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111 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
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112 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
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113 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
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114 count=$((count+1))
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115 done
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116 echo "</table>" >> $outputFile
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117
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118 echo "</html>" >> $outputFile
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