Mercurial > repos > davidvanzessen > igblastn_immunerepertoire_igg

comparison combined.sh @ 0:d52f6a986108 draft

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author davidvanzessen
date Thu, 23 Jan 2014 08:22:28 -0500
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children 7b0d9c107680
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-1:000000000000 0:d52f6a986108
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 function blastAndParse {
16 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html
17 echo "$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"
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
19 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
20
21 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html
22 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > $5
23 echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html
24 }
25
26 id=${inputData[0]}
27 forwardSlash="/"
28 mergerInput=()
29 count=0
30 for current in $inputData; do
31 if [[ "$current" != *"$forwardSlash"* ]]; then
32 id=$current
33 count=0
34 mergerInput+=($id)
35 continue
36 fi
37 fileName=$(basename $current)
38 parsedFileName="${fileName%.*}"
39 parsedFileName="$PWD/$parsedFileName.parsed"
40 blastAndParse $current $id $count $fileName $parsedFileName &
41 mergerInput+=($parsedFileName)
42 count=$((count+1))
43 done
44 wait
45
46
47
48 echo "<tr><td>-----------------------------------</td></tr>" >> $html
49 echo "<tr><td>merging</td></tr>" >> $html
50
51 python $dir/igblastmerge.py ${mergerInput[*]} --output $PWD/merged.txt
52
53 echo "<tr><td>done</td></tr>" >> $html
54 echo "<tr><td>-----------------------------------</td></tr>" >> $html
55 echo "<tr><td>plotting</td></tr>" >> $html
56
57
58 inputFile=$PWD/merged.txt
59 outputFile=$html
60 outputDir=$imageDir
61 mkdir $outputDir
62 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
63 echo "<html>" > $outputFile
64 echo "<img src='VPlot.png'/>" >> $outputFile
65 echo "<img src='DPlot.png'/>" >> $outputFile
66 echo "<img src='JPlot.png'/>" >> $outputFile
67
68 samples=`cat $outputDir/samples.txt`
69 count=1
70 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
71 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
72 for sample in $samples; do
73 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
74 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
75 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
76
77 echo "$hasReplicateColumn"
78 #if its a 'new' merged file with replicate info
79 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
80 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
81
82 #replicate,reads,squared
83 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
84 while IFS=, read replicate reads squared
85 do
86
87 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
88 done < $outputDir/ReplicateReads_$sample.csv
89
90 #sum of reads and reads squared
91 while IFS=, read readsSum squaredSum
92 do
93 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
94 done < $outputDir/ReplicateSumReads_$sample.csv
95
96 echo "</table></td></tr>" >> $outputFile
97
98 #overview
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>" >> $outputFile
100 while IFS=, read type count weight weightedCount
101 do
102 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
103 done < $outputDir/ClonalityOverView_$sample.csv
104 echo "</table></td></tr>" >> $outputFile
105 fi
106
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>" >> $outputFile
108 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
109 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
110 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
111 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
112 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
113 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
114 count=$((count+1))
115 done
116 echo "</table>" >> $outputFile
117
118 echo "</html>" >> $outputFile