Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg
diff complete.sh @ 1:778a9d130904 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 04 Sep 2014 07:46:23 -0400 |
| parents | 7d97fa9a0423 |
| children | 3287f7b9c47d |
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--- a/complete.sh Fri May 09 09:35:32 2014 -0400 +++ b/complete.sh Thu Sep 04 07:46:23 2014 -0400 @@ -1,14 +1,14 @@ #!/bin/bash -clonalType=${@:(-6):1} -html=${@:(-5):1} -imageDir=${@:(-4):1} -species=${@:(-3):1} -locus=${@:(-2):1} -selection=${@:(-1):1} -dataCount=`expr $# - 6` -inputData=${@:(1):dataCount} -echo ${inputData[@]} +inputFiles=($1) +outputDir=$3 +outputFile=$3/index.html #$1 +clonalType=$4 +species=$5 +locus=$6 +selection=$7 + +html=$2 dir="$(cd "$(dirname "$0")" && pwd)" array=("$@") echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html @@ -25,7 +25,7 @@ echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html - perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > $5 + perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > "$5" echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html } @@ -36,17 +36,20 @@ } -id=${inputData[0]} +id="" forwardSlash="/" mergerInput=() -count=0 -for current in $inputData; do - if [[ "$current" != *"$forwardSlash"* ]]; then - id=$current - count=0 - mergerInput+=($id) - continue - fi +echo "Before loop" +count=1 +for current in "${inputFiles[@]}" +do + if [[ "$current" != *"$forwardSlash"* ]]; then + id="$current" + mergerInput+=($id) + count=1 + continue + fi + echo "working on $current" fileName=$(basename $current) parsedFileName="${fileName%.*}" parsedFileName="$PWD/$parsedFileName.parsed" @@ -66,139 +69,28 @@ done wait - +echo "after loop" echo "<tr><td>-----------------------------------</td></tr>" >> $html echo "<tr><td>merging</td></tr>" >> $html -python $dir/igblastmerge.py ${mergerInput[*]} --output $PWD/merged.txt +python $dir/experimental_design.py ${mergerInput[*]} --output $PWD/merged.txt echo "<tr><td>done</td></tr>" >> $html echo "<tr><td>-----------------------------------</td></tr>" >> $html echo "<tr><td>plotting</td></tr>" >> $html - -inputFile=$PWD/merged.txt -outputDir=$imageDir -outputFile=$outputDir/index.html -mkdir $outputDir -Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $selection 2>&1 -cp $dir/tabber.js $outputDir -cp $dir/style.css $outputDir -cp $dir/script.js $outputDir -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 -echo "<html><head><title>Report on:" >> $outputFile -for sample in $samples; do - echo " $sample" >> $outputFile -done -echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile -echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile -echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile -echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile -echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile - -echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile -echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile -echo "<img src='VFPlot.png'/>" >> $outputFile -echo "<img src='DFPlot.png'/>" >> $outputFile -echo "<img src='JFPlot.png'/>" >> $outputFile -echo "<img src='VPlot.png'/>" >> $outputFile -echo "<img src='DPlot.png'/>" >> $outputFile -echo "<img src='JPlot.png'/></div>" >> $outputFile - -samples=`cat $outputDir/samples.txt` -count=1 -echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile -for sample in $samples; do - echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile - - mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" - echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile - mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" - echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile - mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" - echo "<td><img src='DJ_$sample.png'/></td></tr></table></div>" >> $outputFile - count=$((count+1)) -done -echo "</div></div>" >> $outputFile +if [ "$locus" == "igh" ] || [ "$locus" == "igk" ] || [ "$locus" == "igl" ]; then + bash $dir/r_wrapper_b.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $selection +else + bash $dir/r_wrapper_t.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $selection +fi -hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" -#if its a 'new' merged file with replicate info -if [[ "$hasReplicateColumn" == "Yes" ]] ; then - echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile - for sample in $samples; do - clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" - echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile - echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile + - #replicate,reads,squared - echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile - while IFS=, read replicate reads squared - do - - echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile - done < $outputDir/ReplicateReads_$sample.csv - - #sum of reads and reads squared - while IFS=, read readsSum squaredSum - do - echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile - done < $outputDir/ReplicateSumReads_$sample.csv - - #overview - echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile - while IFS=, read type count weight weightedCount - do - echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile - done < $outputDir/ClonalityOverView_$sample.csv - echo "</table></div>" >> $outputFile - done - echo "</div></div>" >> $outputFile -fi -hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" -if [[ "$hasJunctionData" == "Yes" ]] ; then - 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>" >> $outputFile - while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP - do - echo "<tr><td>$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 - done < $outputDir/junctionAnalysis.csv - echo "</tbody></table></div>" >> $outputFile -fi -echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile -for sample in $samples; do - echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile -done -echo "</table><div name='comparisonarea'>" >> $outputFile -echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile -echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile -echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile -echo "</div></div>" >> $outputFile -echo "<div class='tabbertab' title='Downloads'>" >> $outputFile -echo "<table border='1'>" >> $outputFile -echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile -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 -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 -echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile - -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 -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 -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 - -echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile -echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile -echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile - -for sample in $samples; do - 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 - 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 - 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 -done - -echo "</table>" >> $outputFile -echo "</div></html>" >> $outputFile