Mercurial > repos > davidvanzessen > argalaxy_tools

diff report_clonality/r_wrapper.sh~ @ 26:28fbbdfd7a87 draft

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author davidvanzessen
date Mon, 13 Feb 2017 09:08:46 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/r_wrapper.sh~	Mon Feb 13 09:08:46 2017 -0500
@@ -0,0 +1,203 @@
+#!/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
+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 "productive_counting.txt"
+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 "<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'/>" >> $outputFile
+if [[ "$useD" == "true" ]] ; then
+	echo "<img src='DFPlot.png'/>" >> $outputFile
+fi
+echo "<img src='JFPlot.png'/>" >> $outputFile
+echo "<img src='VPlot.png'/>" >> $outputFile
+if [[ "$useD" == "true" ]] ; then
+	echo "<img src='DPlot.png'/>" >> $outputFile
+fi
+echo "<img src='JPlot.png'/>" >> $outputFile
+echo "<img src='AAComposition.png'/></div>" >> $outputFile
+
+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
+
+#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 [[ "$hasReplicateColumn" == "Yes" && "$clonalType" != "none" ]] ; 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 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>" >> $outputFile
+		else
+			echo "in new"
+			clonalityScore="$(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 $inputFile | grep -q '3V-REGION trimmed-nt'; then echo 'Yes'; else echo 'No'; fi)"
+
+if [[ "$hasJunctionData" == "Yes" ]] ; then
+	echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
+	echo "<table border='1' id='junction_table'> <caption>Productive</caption><thead><tr><th>Sample</th><th>count</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/junctionAnalysisProd.csv
+	echo "</tbody></table>" >> $outputFile
+	
+	echo "<table border='1' id='junction_table'> <caption>Unproductive</caption><thead><tr><th>Sample</th><th>count</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/junctionAnalysisUnProd.csv
+	echo "</tbody></table>" >> $outputFile
+	
+	echo "</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>" >> $outputFile
+if [[ "$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 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>" >> $outputFile
+if [[ "$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 "</table>" >> $outputFile
+echo "</div></html>" >> $outputFile