Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/r_wrapper.sh.old @ 20:9185c3dfc679 draft
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author | davidvanzessen |
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date | Fri, 27 Jan 2017 03:44:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/r_wrapper.sh.old Fri Jan 27 03:44:18 2017 -0500 @@ -0,0 +1,315 @@ +#!/bin/bash + +inputFile=$1 +outputDir=$3 +outputFile=$3/index.html #$2 +clonalType=$4 +species=$5 +locus=$6 +filterproductive=$7 +clonality_method=$8 + +dir="$(cd "$(dirname "$0")" && pwd)" +useD="false" +if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then + echo "species D region in reference db" + useD="true" +fi +echo "$species" +if [[ "$species" == *"custom"* ]] ; then + loci=(${locus//;/ }) + useD="true" + echo "${loci[@]}" + if [[ "${#loci[@]}" -eq "2" ]] ; then + useD="false" + fi +fi +mkdir $3 +cp $dir/genes.txt $outputDir +Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1 +cp $dir/tabber.js $outputDir +cp $dir/style.css $outputDir +cp $dir/script.js $outputDir +cp $dir/jquery-1.11.0.min.js $outputDir +cp $dir/pure-min.css $outputDir +samples=`cat $outputDir/samples.txt` + +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)<br />" > $2 +echo "<table border = 1>" >> $2 +echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2 +while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un + do + echo "<tr><td>$sample</td>" >> $2 + echo "<td>$all</td>" >> $2 + echo "<td>$productive (${perc_prod}%)</td>" >> $2 + echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2 + echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2 + echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2 +done < $outputDir/productive_counting.txt +echo "</table border></center></html>" >> $2 + +echo "<html><head><title>Report on:" >> $outputFile + +mkdir $outputDir/circos +cp $dir/circos/* $outputDir/circos/ +#CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" +#CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" + +#CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" +#CIRCOSDIR="/home/galaxy/Anaconda3/bin" + +USECIRCOS="no" +if [ -d "$CIRCOSDIR" ]; then + USECIRCOS="yes" +else + if [ -d "/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" ]; then #hopefully temporary fix + USECIRCOS="yes" + CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" + CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" + fi + + if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix + USECIRCOS="yes" + CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" + CIRCOSDIR="/home/galaxy/Anaconda3/bin" + fi +fi + +echo "Using Circos: $USECIRCOS" +sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf +for sample in $samples; do #output the samples to a file and create the circos plots with the R script output + echo " $sample" >> $outputFile + + if [[ "$USECIRCOS" != "yes" ]]; then + continue + fi + + circos_file="$outputDir/${sample}_VJ_circos.txt" + echo -e -n "labels$(cat ${circos_file})" > ${circos_file} + cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 + mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png + + + if [[ "$useD" == "true" ]] ; then + circos_file="$outputDir/${sample}_VD_circos.txt" + echo -e -n "labels$(cat ${circos_file})" > ${circos_file} + cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 + mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png + + circos_file="$outputDir/${sample}_DJ_circos.txt" + echo -e -n "labels$(cat ${circos_file})" > ${circos_file} + cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 + mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png + + fi +done +echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile +echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $outputFile +echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile +echo "<script type='text/javascript' src='script.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='VFPlot.png'/>" >> $outputFile +if [[ "$useD" == "true" ]] ; then + echo "<img src='DFPlot.png'/>" >> $outputFile +fi +echo "<img src='VPlot.png'/>" >> $outputFile +if [[ "$useD" == "true" ]] ; then + echo "<img src='DPlot.png'/>" >> $outputFile +fi +echo "<img src='JPlot.png'/>" >> $outputFile +echo "</div>" >> $outputFile + +echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile +echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile +echo "<img src='AAComposition.png'/>" >> $outputFile +echo "<img src='DReadingFrame.png'/>" >> $outputFile + +echo "<table class='pure-table pure-table-striped'>" >> $outputFile +echo "<thead><tr><th>Sample</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile +while IFS=, read Sample median +do + echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile +done < $outputDir/AAMedianBySample.csv +echo "</table>" >> $outputFile + +echo "</div>" >> $outputFile + +#Heatmaps + +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>" >> $outputFile + if [[ "$useD" == "true" ]] ; then + echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile + fi + echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile + if [[ "$useD" == "true" ]] ; then + echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile + fi + echo "</tr></table></div>" >> $outputFile + count=$((count+1)) +done +echo "</div></div>" >> $outputFile + +#circos + +if [[ "$USECIRCOS" == "yes" ]]; then + + echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile + for sample in $samples; do + echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile + if [[ "$useD" == "true" ]] ; then + echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile + fi + echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile + if [[ "$useD" == "true" ]] ; then + echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile + fi + echo "<center></table></div>" >> $outputFile + count=$((count+1)) + done + echo "</div></div>" >> $outputFile +fi +#echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile + +hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" +echo "$hasReplicateColumn" +#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 $samples; do + echo "${clonality_method}" + if [[ "${clonality_method}" == "old" ]] ; then + echo "in old" + clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" + echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile + echo "<thead><tr><th colspan='4'>Clonality Score: $clonalityScore</th></tr></thead>" >> $outputFile + + #replicate,reads,squared + echo "<tr><td>Replicate ID</td><td>Number of Reads</td></tr>" >> $outputFile + while IFS=, read replicate reads squared + do + echo "<tr><td>$replicate</td><td>$reads</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></tr>" >> $outputFile + done < $outputDir/ReplicateSumReads_$sample.csv + + #overview + echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td></tr>" >> $outputFile + while IFS=, read type count weight weightedCount + do + if [[ "$type" -eq "1" ]]; then + echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile + else + echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td></tr>" >> $outputFile + fi + + done < $outputDir/ClonalityOverView_$sample.csv + echo "</table></div>" >> $outputFile + else + echo "in new" + clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)" + echo "<div class='tabbertab' title='$sample'>" >> $outputFile + echo "Lymphclon clonality score: <br />$clonalityScore<br /><br />" >> $outputFile + echo "<table border = 1>" >> $outputFile + while IFS=, read type count + do + echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile + done < $outputDir/lymphclon_coincidences_$sample.csv + echo "</table></div>" >> $outputFile + fi + done + echo "</div></div>" >> $outputFile +fi + +#hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)" + +#if [[ "$hasJunctionData" == "Yes" ]] ; then +if [ -a "$outputDir/junctionAnalysisProd_mean.csv" ] ; then + echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median + do + echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile + done < $outputDir/junctionAnalysisProd_mean.csv + echo "</tbody></table>" >> $outputFile + + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median + do + echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile + done < $outputDir/junctionAnalysisUnProd_mean.csv + echo "</tbody></table>" >> $outputFile + + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median + do + echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile + done < $outputDir/junctionAnalysisProd_median.csv + echo "</tbody></table>" >> $outputFile + + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median + do + echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile + done < $outputDir/junctionAnalysisUnProd_median.csv + echo "</tbody></table>" >> $outputFile + + echo "</div>" >> $outputFile +fi + +echo "<div class='tabbertab' title='Comparison'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead>" >> $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 class='pure-table pure-table-striped'>" >> $outputFile +echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $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>" >> $outputFile +if [[ "$useD" == "true" ]] ; then + 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 +fi + +echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile +if [[ "$useD" == "true" ]] ; then + echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile +fi +echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile +echo "<tr><td>The dataset used to generate the AA composition graph</td><td><a href='AAComposition.csv'>Download</a></td></tr>" >> $outputFile + +for sample in $samples; do + if [[ "$useD" == "true" ]] ; then + 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 + fi + echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile + if [[ "$useD" == "true" ]] ; then + 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 + fi +done + +echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href='VJCDR3_count.txt'>Download</a></td></tr>" >> $outputFile + +echo "</table>" >> $outputFile +echo "</div></html>" >> $outputFile