Mercurial > repos > davidvanzessen > combined_immune_repertoire_imgt

comparison combined.sh @ 1:d2b3bcabb478 draft

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author davidvanzessen
date Mon, 09 Dec 2013 06:08:52 -0500
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children 8ba0fd5b03a1
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0:e71c59b72669 1:d2b3bcabb478
1 #!/bin/bash
2
3 export IGDATA=/home/david/tmp/ncbi-igblast-1.0.0;
4
5 clonalType=${@:(-3):1}
6 html=${@:(-2):1}
7 imageDir=${@:(-1):1}
8 dataCount=`expr $# - 3`
9 inputData=${@:(1):dataCount}
10 dir="$(cd "$(dirname "$0")" && pwd)"
11 array=("$@")
12 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
13 echo "<tr><td>-----------------------------------</td></tr>" >> $html
14
15 id=${inputData[0]}
16 forwardSlash="/"
17 mergerInput=()
18 count=0
19 for current in $inputData; do
20 if [[ "$current" != *"$forwardSlash"* ]]; then
21 id=$current
22 count=0
23 mergerInput+=($id)
24 continue
25 fi
26 fileName=$(basename $current)
27 convertedFileName="${fileName%.*}"
28 convertedFileName="$PWD/$convertedFileName.converted"
29 bash $dir/imgtconvert.sh $current $id $count $convertedFileName
30 mergerInput+=($convertedFileName)
31 count=$((count+1))
32 done
33 wait
34
35
36
37 echo "<tr><td>-----------------------------------</td></tr>" >> $html
38 echo "<tr><td>merging</td></tr>" >> $html
39
40 python $dir/igblastmerge.py ${mergerInput[*]} --output $PWD/merged.txt
41
42 echo "<tr><td>done</td></tr>" >> $html
43 echo "<tr><td>-----------------------------------</td></tr>" >> $html
44 echo "<tr><td>plotting</td></tr>" >> $html
45
46
47 inputFile=$PWD/merged.txt
48 outputFile=$html
49 outputDir=$imageDir
50 mkdir $outputDir
51 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
52 echo "<html>" > $outputFile
53 echo "<img src='VPlot.png'/>" >> $outputFile
54 echo "<img src='DPlot.png'/>" >> $outputFile
55 echo "<img src='JPlot.png'/>" >> $outputFile
56
57 samples=`cat $outputDir/samples.txt`
58 count=1
59 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
60 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
61 for sample in $samples; do
62 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
63 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
64 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
65
66 echo "$hasReplicateColumn"
67 #if its a 'new' merged file with replicate info
68 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
69 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
70
71 #replicate,reads,squared
72 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
73 while IFS=, read replicate reads squared
74 do
75
76 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
77 done < $outputDir/ReplicateReads_$sample.csv
78
79 #sum of reads and reads squared
80 while IFS=, read readsSum squaredSum
81 do
82 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
83 done < $outputDir/ReplicateSumReads_$sample.csv
84
85 echo "</table></td></tr>" >> $outputFile
86
87 #overview
88 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>" >> $outputFile
89 while IFS=, read type count weight weightedCount
90 do
91 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
92 done < $outputDir/ClonalityOverView_$sample.csv
93 echo "</table></td></tr>" >> $outputFile
94 fi
95
96 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>" >> $outputFile
97 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
98 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
99 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
100 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
101 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
102 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
103 count=$((count+1))
104 done
105 echo "</table>" >> $outputFile
106
107 echo "</html>" >> $outputFile