Mercurial > repos > davidvanzessen > igblastn_immunerepertoire_igg

comparison combined.sh @ 5:be7ed742f870 draft default tip

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author davidvanzessen
date Tue, 11 Mar 2014 11:10:30 -0400
parents 2f2544607ad6
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comparison
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4:2f2544607ad6 5:be7ed742f870
15 export IGDATA=$PWD/igblastdatabase/ 15 export IGDATA=$PWD/igblastdatabase/
16 16
17 function blastAndParse { 17 function blastAndParse {
18 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html 18 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html
19 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" 19 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"
20 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 20 /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
21 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html 21 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
22 22
23 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html 23 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html
24 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > $5 24 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > $5
25 echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html 25 echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html
56 echo "<tr><td>-----------------------------------</td></tr>" >> $html 56 echo "<tr><td>-----------------------------------</td></tr>" >> $html
57 echo "<tr><td>plotting</td></tr>" >> $html 57 echo "<tr><td>plotting</td></tr>" >> $html
58 58
59 59
60 inputFile=$PWD/merged.txt 60 inputFile=$PWD/merged.txt
61 outputFile=$html
62 outputDir=$imageDir 61 outputDir=$imageDir
62 outputFile=$outputDir/index.html
63 mkdir $outputDir 63 mkdir $outputDir
64 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1 64 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
65 echo "<html>" > $outputFile 65 cp $dir/tabber.js $outputDir
66 cp $dir/style.css $outputDir
67 cp $dir/script.js $outputDir
68 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
69 echo "<html><script type='text/javascript' src='tabber.js'></script><script type='text/javascript' src='script.js'></script><link rel='stylesheet' type='text/css' href='style.css'><div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
66 echo "<img src='VPlot.png'/>" >> $outputFile 70 echo "<img src='VPlot.png'/>" >> $outputFile
67 echo "<img src='DPlot.png'/>" >> $outputFile 71 echo "<img src='DPlot.png'/>" >> $outputFile
68 echo "<img src='JPlot.png'/>" >> $outputFile 72 echo "<img src='JPlot.png'/></div>" >> $outputFile
69 73
70 samples=`cat $outputDir/samples.txt` 74 samples=`cat $outputDir/samples.txt`
71 count=1 75 count=1
72 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile 76 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
77 for sample in $samples; do
78 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
79
80 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
81 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
82 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
83 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
84 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
85 echo "<td><img src='DJ_$sample.png'/></td></tr></table></div>" >> $outputFile
86 count=$((count+1))
87 done
88 echo "</div></div>" >> $outputFile
89
90
73 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" 91 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
74 for sample in $samples; do 92 echo "$hasReplicateColumn"
75 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" 93 #if its a 'new' merged file with replicate info
76 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile 94 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
77 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile 95 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
78 96 for sample in $samples; do
79 echo "$hasReplicateColumn" 97 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
80 #if its a 'new' merged file with replicate info 98 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
81 if [[ "$hasReplicateColumn" == "Yes" ]] ; then 99 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
82 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
83 100
84 #replicate,reads,squared 101 #replicate,reads,squared
85 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile 102 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
86 while IFS=, read replicate reads squared 103 while IFS=, read replicate reads squared
87 do 104 do
88 105
89 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile 106 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
90 done < $outputDir/ReplicateReads_$sample.csv 107 done < $outputDir/ReplicateReads_$sample.csv
91 108
92 #sum of reads and reads squared 109 #sum of reads and reads squared
93 while IFS=, read readsSum squaredSum 110 while IFS=, read readsSum squaredSum
94 do 111 do
95 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile 112 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
96 done < $outputDir/ReplicateSumReads_$sample.csv 113 done < $outputDir/ReplicateSumReads_$sample.csv
97 114
98 echo "</table></td></tr>" >> $outputFile
99
100 #overview 115 #overview
101 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 116 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
102 while IFS=, read type count weight weightedCount 117 while IFS=, read type count weight weightedCount
103 do 118 do
104 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile 119 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
105 done < $outputDir/ClonalityOverView_$sample.csv 120 done < $outputDir/ClonalityOverView_$sample.csv
106 echo "</table></td></tr>" >> $outputFile 121 echo "</table></div>" >> $outputFile
107 fi 122 done
123 echo "</div></div>" >> $outputFile
124 fi
108 125
109 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>" >> $outputFile 126
110 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" 127 hasFunctionalityColumn="$(if head -n 1 $inputFile | grep -q 'Functionality'; then echo 'Yes'; else echo 'No'; fi)"
111 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile 128 if [[ "$hasFunctionalityColumn" == "Yes" ]] ; then
112 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" 129 echo "<div class='tabbertab' title='Junction Analysis'><table border='1'><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></tr>" >> $outputFile
113 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile 130 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
114 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" 131 do
115 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile 132 echo "<tr><td>$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>" >> $outputFile
116 count=$((count+1)) 133 done < $outputDir/junctionAnalysis.csv
134 echo "</table></div>" >> $outputFile
135 fi
136
137 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
138 for sample in $samples; do
139 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
117 done 140 done
141 echo "</table><div name='comparisonarea'>" >> $outputFile
142 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
143 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
144 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
145 echo "</div></div>" >> $outputFile
146
147 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
148 echo "<table border='1'>" >> $outputFile
149 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile
150 echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.tsv'>Download</a></td></tr>" >> $outputFile
151 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.tsv'>Download</a></td></tr>" >> $outputFile
118 echo "</table>" >> $outputFile 152 echo "</table>" >> $outputFile
119 153 echo "</div>" >> $outputFile
120 echo "</html>" >> $outputFile