Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline

comparison combined.sh @ 0:4e3df2384422 draft

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author davidvanzessen
date Wed, 20 Nov 2013 10:00:28 -0500
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children 9b2567a3ecc9
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-1:000000000000 0:4e3df2384422
1 #!/bin/bash
2
3 export IGDATA=/home/david/Galaxy/galaxy-dist/toolsheddependencies/igBlastn/1.0.0/davidvanzessen/igblast_human/1c64c977624e/ncbi-igblast-1.0.0/;
4
5 html=${@:(-2):1}
6 imageDir=${@:(-1):1}
7 dir="$(cd "$(dirname "$0")" && pwd)"
8 fileCount=`expr $# - 2`
9 array=("$@")
10 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
11 echo "<tr><td>-----------------------------------</td></tr>" >> $html
12 limit=`expr $fileCount / 2`
13
14 function blastAndParse {
15 echo "<tr><td>Starting blast of $2</td></tr>" >> $html
16 fileName=$(basename $1)
17 $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 > $PWD/$fileName
18 echo "<tr><td>Finished blast of $2</td></tr>" >> $html
19
20 echo "<tr><td>Starting parse of $2</td></tr>" >> $html
21 parsedFileName="${fileName%.*}"
22 parsedFileName="$parsedFileName.parsed"
23 perl $dir/igparse.pl $PWD/$fileName 0 | grep -v "D:" | cut -f2- > $parsedFileName
24 echo "<tr><td>Finished parse of $2</td></tr>" >> $html
25 }
26
27 for ((i=0;i<$fileCount;i=$((i+2))))
28 do
29 next=$((i+1))
30 blastAndParse ${array[$i]} ${array[$next]} &
31 done
32 wait
33
34
35
36 echo "<tr><td>-----------------------------------</td></tr>" >> $html
37 echo "<tr><td>merging</td></tr>" >> $html
38
39 count=0
40 for ((i=0;i<$fileCount;i=$((i+2))))
41 do
42 id=$((i+1))
43 place=$((count+limit))
44 fn=$(basename ${array[$i]})
45 fn="${fn%.*}"
46 mergeInputs[$count]="$PWD/$fn.parsed"
47 mergeIDs[$place]=${array[$id]}
48 count=$((count+1))
49 done
50
51 python $dir/igblastmerge.py --input ${mergeInputs[*]} --id ${mergeIDs[*]} --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 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'>" >> $outputFile
71 for sample in $samples; do
72 echo "<tr><td colspan='3' height='100'></td>" >> $outputFile
73 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
74 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>" >> $outputFile
75 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
76 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
77 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
78 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
79 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
80 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
81 count=$((count+1))
82 done
83 echo "</table>" >> $outputFile
84
85 echo "</html>" >> $2
86
87
88 #r_wrapper.sh $in_file $out_file $out_file.files_path
89
90 echo "<tr><td>done</td></tr>" >> $html