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1 #!/bin/bash
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2
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3 clonalType=${@:(-6):1}
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4 html=${@:(-5):1}
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5 imageDir=${@:(-4):1}
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6 species=${@:(-3):1}
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7 locus=${@:(-2):1}
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8 selection=${@:(-1):1}
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9 dataCount=`expr $# - 6`
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10 inputData=${@:(1):dataCount}
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11 echo ${inputData[@]}
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12 dir="$(cd "$(dirname "$0")" && pwd)"
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13 array=("$@")
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14 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
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15 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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16
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17 mkdir $PWD/igblastdatabase
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18 unzip $dir/database.zip -d $PWD/igblastdatabase/
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19 export IGDATA=$PWD/igblastdatabase/
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20
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21 function blastAndParse {
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22 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html
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23 echo "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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24 /home/galaxy/galaxy/igblast/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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25 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
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26
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27 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html
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28 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > $5
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29 echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html
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30 }
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31
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32 function imgtConvert {
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33 echo "<tr><td>Starting imgt convert of sample $3 of patient $2</td></tr>" >> $html
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34 bash $dir/imgtconvert.sh $1 $2 $3 $4
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35 echo "<tr><td>Finished conversion of sample $3 of patient $2</td></tr>" >> $html
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36
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37 }
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38
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39 id=${inputData[0]}
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40 forwardSlash="/"
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41 mergerInput=()
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42 count=0
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43 for current in $inputData; do
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44 if [[ "$current" != *"$forwardSlash"* ]]; then
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45 id=$current
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46 count=0
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47 mergerInput+=($id)
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48 continue
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49 fi
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50 fileName=$(basename $current)
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51 parsedFileName="${fileName%.*}"
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52 parsedFileName="$PWD/$parsedFileName.parsed"
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53 f=$(file $current)
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54 zipType="Zip archive"
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55 if [[ "$f" == *"$zipType"* ]]
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56 then
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57 echo "<tr><td>Sample $count of patient $id is a zip file, using IMGT Loader</td></tr>" >> $html
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58 fileName=$(basename $current)
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59 imgtConvert $current $id $count $parsedFileName &
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60 else
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61 echo "<tr><td>Sample $count of patient $id is not a zip file, using igBLASTn</td></tr>" >> $html
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62 blastAndParse $current $id $count $fileName $parsedFileName &
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63 fi
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64 mergerInput+=($parsedFileName)
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65 count=$((count+1))
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66 done
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67 wait
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68
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69
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70
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71 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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72 echo "<tr><td>merging</td></tr>" >> $html
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73
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74 python $dir/igblastmerge.py ${mergerInput[*]} --output $PWD/merged.txt
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75
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76 echo "<tr><td>done</td></tr>" >> $html
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77 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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78 echo "<tr><td>plotting</td></tr>" >> $html
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79
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80
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81 inputFile=$PWD/merged.txt
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82 outputDir=$imageDir
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83 outputFile=$outputDir/index.html
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84 mkdir $outputDir
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85 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $selection 2>&1
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86 cp $dir/tabber.js $outputDir
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87 cp $dir/style.css $outputDir
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88 cp $dir/script.js $outputDir
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89 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)</center></html>" > $html
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90 echo "<html><head><title>Report on:" >> $outputFile
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91 for sample in $samples; do
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92 echo " $sample" >> $outputFile
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93 done
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94 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
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95 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
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96 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
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97 echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile
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98 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
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99
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100 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
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101 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
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102 echo "<img src='VFPlot.png'/>" >> $outputFile
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103 echo "<img src='DFPlot.png'/>" >> $outputFile
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104 echo "<img src='JFPlot.png'/>" >> $outputFile
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105 echo "<img src='VPlot.png'/>" >> $outputFile
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106 echo "<img src='DPlot.png'/>" >> $outputFile
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107 echo "<img src='JPlot.png'/></div>" >> $outputFile
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108
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109 samples=`cat $outputDir/samples.txt`
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110 count=1
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111 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
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112 for sample in $samples; do
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113 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
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114
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115 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
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116 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
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117 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
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118 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
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119 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
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120 echo "<td><img src='DJ_$sample.png'/></td></tr></table></div>" >> $outputFile
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121 count=$((count+1))
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122 done
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123 echo "</div></div>" >> $outputFile
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124
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125
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126 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
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127 #if its a 'new' merged file with replicate info
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128 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
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129 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
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130 for sample in $samples; do
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131 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
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132 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
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133 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
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134
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135 #replicate,reads,squared
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136 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
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137 while IFS=, read replicate reads squared
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138 do
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139
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140 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
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141 done < $outputDir/ReplicateReads_$sample.csv
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142
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143 #sum of reads and reads squared
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144 while IFS=, read readsSum squaredSum
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145 do
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146 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
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147 done < $outputDir/ReplicateSumReads_$sample.csv
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148
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149 #overview
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150 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
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151 while IFS=, read type count weight weightedCount
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152 do
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153 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
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154 done < $outputDir/ClonalityOverView_$sample.csv
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155 echo "</table></div>" >> $outputFile
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156 done
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157 echo "</div></div>" >> $outputFile
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158 fi
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159
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160 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"
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161
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162 if [[ "$hasJunctionData" == "Yes" ]] ; then
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163 echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table' class='tablesorter'><thead><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
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164 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
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165 do
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166 echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
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167 done < $outputDir/junctionAnalysis.csv
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168 echo "</tbody></table></div>" >> $outputFile
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169 fi
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170
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171 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
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172 for sample in $samples; do
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173 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
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174 done
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175 echo "</table><div name='comparisonarea'>" >> $outputFile
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176 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
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177 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
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178 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
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179 echo "</div></div>" >> $outputFile
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180
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181 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
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182 echo "<table border='1'>" >> $outputFile
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183 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile
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184 echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>Download</a></td></tr>" >> $outputFile
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185 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.csv'>Download</a></td></tr>" >> $outputFile
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186
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187 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
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188
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189 echo "<tr><td>The dataset used to generate the V gene family frequency graph</td><td><a href='VFFrequency.csv'>Download</a></td></tr>" >> $outputFile
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190 echo "<tr><td>The dataset used to generate the D gene family frequency graph</td><td><a href='DFFrequency.csv'>Download</a></td></tr>" >> $outputFile
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191 echo "<tr><td>The dataset used to generate the J gene family frequency graph</td><td><a href='JFFrequency.csv'>Download</a></td></tr>" >> $outputFile
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192
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193 echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile
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194 echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile
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195 echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile
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196
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197 for sample in $samples; do
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198 echo "<tr><td>The data used to generate the VD heatmap for $sample.</td><td><a href='HeatmapVD_$sample.csv'>Download</a></td></tr>" >> $outputFile
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199 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
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200 echo "<tr><td>The data used to generate the DJ heatmap for $sample.</td><td><a href='HeatmapDJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
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201 done
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202
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203 echo "</table>" >> $outputFile
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204 echo "</div></html>" >> $outputFile
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