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.gitattributes complete.sh experimental_design/experimental_design.sh igblast/igblast.sh imgt_loader/imgt_loader.sh report_clonality/r_wrapper.sh |
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| diff -r 124b7fd92a3e -r 0ef7f80ea061 .gitattributes --- a/.gitattributes Thu Feb 25 13:36:15 2021 +0000 +++ b/.gitattributes Thu Feb 25 13:39:50 2021 +0000 |
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| @@ -1,2 +1,4 @@ # Auto detect text files and perform LF normalization * text=auto +# Convert to LF line endings on checkout. +*.sh text eol=lf |
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| diff -r 124b7fd92a3e -r 0ef7f80ea061 complete.sh --- a/complete.sh Thu Feb 25 13:36:15 2021 +0000 +++ b/complete.sh Thu Feb 25 13:39:50 2021 +0000 |
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| @@ -1,72 +1,72 @@ -#!/bin/bash -set -e -inputFiles=($1) -outputDir=$3 -outputFile=$3/index.html #$1 -clonalType=$4 -species=$5 -locus=$6 -filterproductive=$7 -clonality_method=$8 - -html=$2 -dir="$(cd "$(dirname "$0")" && pwd)" -array=("$@") -echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html -echo "<tr><td>-----------------------------------</td></tr>" >> $html - -#mkdir $PWD/igblastdatabase -#unzip $dir/database.zip -d $PWD/igblastdatabase/ -#export IGDATA=$PWD/igblastdatabase/ - -echo "python: `which python`" -echo "R: `which R`" -echo "Rscript: `which Rscript`" - -id="" -forwardSlash="/" -mergerInput=() -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 $current) - fileName="${fileName%.*}" - parsedFileName="$PWD/$fileName.parsed" - f=$(file $current) - zipType="Zip archive" - zxType="XZ compressed data" - echo "filetype of ${id}: $f" - if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]] - then - echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html - fileName=$(basename $current) - bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}" - else - echo "<tr><td>Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn</td></tr>" >> $html - bash ${dir}/igblast/igblast.sh $current "$species" $locus $parsedFileName - fi - mergerInput+=($parsedFileName) - count=$((count+1)) -done - -echo "<tr><td>-----------------------------------</td></tr>" >> $html -echo "<tr><td>merging</td></tr>" >> $html - -bash $dir/experimental_design/experimental_design.sh ${mergerInput[*]} $PWD/merged.txt - -echo "<tr><td>done</td></tr>" >> $html -echo "<tr><td>-----------------------------------</td></tr>" >> $html -echo "<tr><td>plotting</td></tr>" >> $html - -echo "after ED" - -bash $dir/report_clonality/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" "$locus" $filterproductive $clonality_method - +#!/bin/bash +set -e +inputFiles=($1) +outputDir=$3 +outputFile=$3/index.html #$1 +clonalType=$4 +species=$5 +locus=$6 +filterproductive=$7 +clonality_method=$8 + +html=$2 +dir="$(cd "$(dirname "$0")" && pwd)" +array=("$@") +echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html +echo "<tr><td>-----------------------------------</td></tr>" >> $html + +#mkdir $PWD/igblastdatabase +#unzip $dir/database.zip -d $PWD/igblastdatabase/ +#export IGDATA=$PWD/igblastdatabase/ + +echo "python: `which python`" +echo "R: `which R`" +echo "Rscript: `which Rscript`" + +id="" +forwardSlash="/" +mergerInput=() +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 $current) + fileName="${fileName%.*}" + parsedFileName="$PWD/$fileName.parsed" + f=$(file $current) + zipType="Zip archive" + zxType="XZ compressed data" + echo "filetype of ${id}: $f" + if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]] + then + echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html + fileName=$(basename $current) + bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}" + else + echo "<tr><td>Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn</td></tr>" >> $html + bash ${dir}/igblast/igblast.sh $current "$species" $locus $parsedFileName + fi + mergerInput+=($parsedFileName) + count=$((count+1)) +done + +echo "<tr><td>-----------------------------------</td></tr>" >> $html +echo "<tr><td>merging</td></tr>" >> $html + +bash $dir/experimental_design/experimental_design.sh ${mergerInput[*]} $PWD/merged.txt + +echo "<tr><td>done</td></tr>" >> $html +echo "<tr><td>-----------------------------------</td></tr>" >> $html +echo "<tr><td>plotting</td></tr>" >> $html + +echo "after ED" + +bash $dir/report_clonality/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" "$locus" $filterproductive $clonality_method + |
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| diff -r 124b7fd92a3e -r 0ef7f80ea061 experimental_design/experimental_design.sh --- a/experimental_design/experimental_design.sh Thu Feb 25 13:36:15 2021 +0000 +++ b/experimental_design/experimental_design.sh Thu Feb 25 13:39:50 2021 +0000 |
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| @@ -1,4 +1,4 @@ - -dir="$(cd "$(dirname "$0")" && pwd)" - -Rscript --verbose $dir/experimental_design.r $@ 2>&1 + +dir="$(cd "$(dirname "$0")" && pwd)" + +Rscript --verbose $dir/experimental_design.r $@ 2>&1 |
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| diff -r 124b7fd92a3e -r 0ef7f80ea061 igblast/igblast.sh --- a/igblast/igblast.sh Thu Feb 25 13:36:15 2021 +0000 +++ b/igblast/igblast.sh Thu Feb 25 13:39:50 2021 +0000 |
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| @@ -1,28 +1,28 @@ -set -e - -dir="$(cd "$(dirname "$0")" && pwd)" - -input=$1 -species=$2 -locus=$3 -output=$4 - -declare -A speciesdict - -speciesdict=(["Rattus norvegicus functional"]="rat" ["Rattus norvegicus non-functional"]="rat" ["Oryctolagus cuniculus functional"]="rabbit" ["Oryctolagus cuniculus non-functional"]="rabbit" ["Mus musculus functional"]="mouse" ["Mus musculus non-functional"]="mouse" ["Homo sapiens functional"]="human" ["Homo sapiens non-functional"]="human" ["Macaca mulatta non-functional"]="rhesus_monkey" ["Macaca mulatta functional"]="rhesus_monkey") - -echo "Species: $species ${speciesdict[$species]}" - -species="${speciesdict[$species]}" - -if [ "$species" == "" ] -then - >&2 echo "Species not possible with igBLASTn, use IMGT" - exit 1 -fi - -echo "$input $species $locus $output" - -java -Xmx16G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1 - -Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1 +set -e + +dir="$(cd "$(dirname "$0")" && pwd)" + +input=$1 +species=$2 +locus=$3 +output=$4 + +declare -A speciesdict + +speciesdict=(["Rattus norvegicus functional"]="rat" ["Rattus norvegicus non-functional"]="rat" ["Oryctolagus cuniculus functional"]="rabbit" ["Oryctolagus cuniculus non-functional"]="rabbit" ["Mus musculus functional"]="mouse" ["Mus musculus non-functional"]="mouse" ["Homo sapiens functional"]="human" ["Homo sapiens non-functional"]="human" ["Macaca mulatta non-functional"]="rhesus_monkey" ["Macaca mulatta functional"]="rhesus_monkey") + +echo "Species: $species ${speciesdict[$species]}" + +species="${speciesdict[$species]}" + +if [ "$species" == "" ] +then + >&2 echo "Species not possible with igBLASTn, use IMGT" + exit 1 +fi + +echo "$input $species $locus $output" + +java -Xmx16G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1 + +Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1 |
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| diff -r 124b7fd92a3e -r 0ef7f80ea061 imgt_loader/imgt_loader.sh --- a/imgt_loader/imgt_loader.sh Thu Feb 25 13:36:15 2021 +0000 +++ b/imgt_loader/imgt_loader.sh Thu Feb 25 13:39:50 2021 +0000 |
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| @@ -1,74 +1,74 @@ -#!/bin/bash -input=$1 -output=$2 -name=$3 -dir="$(cd "$(dirname "$0")" && pwd)" -mkdir -p $PWD/$name/files -f=$(file $input) -zip7Type="7-zip archive" -tarType="tar archive" -bzip2Type="bzip2 compressed" -gzipType="gzip compressed" -zipType="Zip archive" -rarType="RAR archive" -zxType="XZ compressed data" - -if [[ "$f" == *"$zip7Type"* ]]; then - echo "7-zip" - echo "Trying: 7za e $input -o$PWD/files/" - 7za e $input -o$PWD/$name/files -fi - -if [[ "$f" == *"$tarType"* ]] -then - echo "tar archive" - echo "Trying: tar xvf $input -C $PWD/files/" - tar -xvf $input -C $PWD/$name/files -fi - -if [[ "$f" == *"$bzip2Type"* ]] -then - echo "bzip2 compressed data" - echo "Trying: tar jxf $input -C $PWD/files/" - tar -jxf $input -C $PWD/$name/files -fi - -if [[ "$f" == *"$gzipType"* ]] -then - echo "gzip compressed data" - echo "Trying: tar xvzf $input -C $PWD/files/" - tar -xvzf $input -C $PWD/$name/files -fi - -if [[ "$f" == *"$zipType"* ]] -then - echo "Zip archive" - echo "Trying: unzip $input -d $PWD/files/" - unzip $input -d $PWD/$name/files > $PWD/unziplog.log -fi - -if [[ "$f" == *"$rarType"* ]] -then - echo "RAR archive" - echo "Trying: unrar e $input $PWD/files/" - unrar e $input $PWD/$name/files -fi - -if [[ "$f" == *"$zxType"* ]] -then - echo "xz compressed data" - echo "Trying: tar -xJf $input -C $PWD/files/" - tar xJf $input -C $PWD/$name/files -fi -find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt -find $PWD/$name/files -iname "3_*" -exec cat {} + > $PWD/$name/sequences.txt -find $PWD/$name/files -iname "4_*" -exec cat {} + > $PWD/$name/gapped_aa.txt -find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt -find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt - -echo "summ.txt `cat $PWD/$name/summ.txt | wc -l`" -echo "aa.txt `cat $PWD/$name/aa.txt | wc -l`" - -#python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output - -Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/sequences.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $PWD/$name/gapped_aa.txt $output 2>&1 +#!/bin/bash +input=$1 +output=$2 +name=$3 +dir="$(cd "$(dirname "$0")" && pwd)" +mkdir -p $PWD/$name/files +f=$(file $input) +zip7Type="7-zip archive" +tarType="tar archive" +bzip2Type="bzip2 compressed" +gzipType="gzip compressed" +zipType="Zip archive" +rarType="RAR archive" +zxType="XZ compressed data" + +if [[ "$f" == *"$zip7Type"* ]]; then + echo "7-zip" + echo "Trying: 7za e $input -o$PWD/files/" + 7za e $input -o$PWD/$name/files +fi + +if [[ "$f" == *"$tarType"* ]] +then + echo "tar archive" + echo "Trying: tar xvf $input -C $PWD/files/" + tar -xvf $input -C $PWD/$name/files +fi + +if [[ "$f" == *"$bzip2Type"* ]] +then + echo "bzip2 compressed data" + echo "Trying: tar jxf $input -C $PWD/files/" + tar -jxf $input -C $PWD/$name/files +fi + +if [[ "$f" == *"$gzipType"* ]] +then + echo "gzip compressed data" + echo "Trying: tar xvzf $input -C $PWD/files/" + tar -xvzf $input -C $PWD/$name/files +fi + +if [[ "$f" == *"$zipType"* ]] +then + echo "Zip archive" + echo "Trying: unzip $input -d $PWD/files/" + unzip $input -d $PWD/$name/files > $PWD/unziplog.log +fi + +if [[ "$f" == *"$rarType"* ]] +then + echo "RAR archive" + echo "Trying: unrar e $input $PWD/files/" + unrar e $input $PWD/$name/files +fi + +if [[ "$f" == *"$zxType"* ]] +then + echo "xz compressed data" + echo "Trying: tar -xJf $input -C $PWD/files/" + tar xJf $input -C $PWD/$name/files +fi +find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt +find $PWD/$name/files -iname "3_*" -exec cat {} + > $PWD/$name/sequences.txt +find $PWD/$name/files -iname "4_*" -exec cat {} + > $PWD/$name/gapped_aa.txt +find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt +find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt + +echo "summ.txt `cat $PWD/$name/summ.txt | wc -l`" +echo "aa.txt `cat $PWD/$name/aa.txt | wc -l`" + +#python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output + +Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/sequences.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $PWD/$name/gapped_aa.txt $output 2>&1 |
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| diff -r 124b7fd92a3e -r 0ef7f80ea061 report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Thu Feb 25 13:36:15 2021 +0000 +++ b/report_clonality/r_wrapper.sh Thu Feb 25 13:39:50 2021 +0000 |
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| b'@@ -1,391 +1,391 @@\n-#!/bin/bash\r\n-\r\n-inputFile=$1\r\n-outputDir=$3\r\n-outputFile=$3/index.html #$2\r\n-clonalType=$4\r\n-species=$5\r\n-locus=$6\r\n-filterproductive=$7\r\n-clonality_method=$8\r\n-\r\n-dir="$(cd "$(dirname "$0")" && pwd)"\r\n-useD="false"\r\n-if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then\r\n-\techo "species D region in reference db"\r\n-\tuseD="true"\r\n-fi\r\n-echo "$species"\r\n-if [[ "$species" == *"custom"* ]] ; then\r\n-\tloci=(${locus//;/ })\r\n-\tuseD="true"\r\n-\techo "${loci[@]}"\r\n-\tif [[ "${#loci[@]}" -eq "2" ]] ; then\r\n-\t\tuseD="false"\r\n-\tfi\r\n-fi\r\n-mkdir $3\r\n-cp $dir/genes.txt $outputDir\r\n-Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1\r\n-cp $dir/tabber.js $outputDir\r\n-cp $dir/style.css $outputDir\r\n-cp $dir/script.js $outputDir\r\n-cp $dir/jquery-1.11.0.min.js $outputDir\r\n-cp $dir/pure-min.css $outputDir\r\n-cp $dir/IGH_junctie_analyse.png $outputDir\r\n-samples=`cat $outputDir/samples.txt`\r\n-\r\n-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\r\n-echo "<table border = 1>" >> $2\r\n-echo "<thead><tr><th>Donor/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2\r\n-while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un\r\n-\tdo\r\n-\t\techo "<tr><td>$sample</td>" >> $2\r\n-\t\techo "<td>$all</td>" >> $2\r\n-\t\tif [[ "$productive" != "0" ]] ; then\r\n-\t\t\techo "<td>$productive (${perc_prod}%)</td>" >> $2\r\n-\t\t\techo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2\r\n-\t\t\techo "<td>$unproductive (${perc_unprod}%)</td>" >> $2\r\n-\t\t\techo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2\r\n-\t\telse\r\n-\t\t\techo "<td colspan=\'4\' style=\'background-color: red;\'>No productive sequences!</td>" >> $2\r\n-\t\tfi\r\n-done < $outputDir/productive_counting.txt\r\n-echo "</table><br />" >> $2\r\n-echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate. <br />" >> $2\r\n-echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2\r\n-echo "</center></html>" >> $2\r\n-\r\n-echo "<html><head><title>Report on:" >> $outputFile\r\n-\r\n-mkdir $outputDir/circos\r\n-cp -R $dir/circos/* $outputDir/circos/\r\n-\r\n-USECIRCOS="no"\r\n-path_to_circos=$(which circos)\r\n-if [ -x "$path_to_circos" ]; then\r\n-\tUSECIRCOS="yes"\r\n-fi\r\n-\r\n-echo "Using Circos: $USECIRCOS"\r\n-sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf\r\n-for sample in $samples; do #output the samples to a file and create the circos plots with the R script output\r\n-\techo " $sample" >> $outputFile\r\n-\t\r\n-\tif [[ "$USECIRCOS" != "yes" ]]; then\r\n-\t\tcontinue\r\n-\tfi\r\n-\t\r\n-\tcircos_file="$outputDir/${sample}_VJ_circos.txt"\r\n-\tsed -i -- \'s%/%:%g\' $circos_file\r\n-\techo -e -n "labels$(cat ${circos_file})" > ${circos_file}\r\n-\techo "Circos tools command:"\r\n-\techo "cat \\"${circos_file}\\" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/"\r\n-\tcat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/\r\n-\r\n-\techo "Circos command:"\r\n-\techo "circos -conf $outputDir/circos/circos.conf 2>&1"\r\n-\tcircos -conf $outputDir/circos/circos.conf 2>&1\r\n-\tmv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png\r\n-\tmv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg\r\n-\t\r\n-\t\r\n-\tif [[ "$useD" == "true" ]] ; then\r\n-\t\tcircos_file="$outputDir/${sample}_VD_circos.txt"\r\n-\t\tsed -i -- \'s%/%:%g\' $circos_file\r\n-\t\techo -e -n "labels$(cat ${circos_file})" > ${circos_file}\r\n-\t\tcat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/\r\n-\t\tsed -i -- \'s%/%:%g\' $outputDir'..b' $outputFile\n+\t\n+\techo "</div>" >> $outputFile\n+fi\n+\n+echo "<div class=\'tabbertab\' title=\'Downloads\'>" >> $outputFile\n+echo "<table class=\'pure-table pure-table-striped\'>" >> $outputFile\n+echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile\n+echo "<tr><td>The filtered dataset</td><td><a href=\'allUnique.txt\'>Download</a></td></tr>" >> $outputFile\n+echo "<tr><td colspan=\'2\' style=\'background-color:#E0E0E0;\'>Gene frequencies</td></tr>" >> $outputFile\n+\n+echo "<tr><td>The dataset used to generate the distribution of V gene families graph</td><td><a href=\'VFFrequency.txt\'>Download</a></td></tr>" >> $outputFile\n+if [[ "$useD" == "true" ]] ; then\n+\techo "<tr><td>The dataset used to generate the distribution of D gene families graph</td><td><a href=\'DFFrequency.txt\'>Download</a></td></tr>" >> $outputFile\n+fi\n+\n+echo "<tr><td>The dataset used to generate the relative frequency of V gene usage graph</td><td><a href=\'VFrequency.txt\'>Download</a></td></tr>" >> $outputFile\n+if [[ "$useD" == "true" ]] ; then\n+\techo "<tr><td>The dataset used to generate the relative frequency of D gene usage graph</td><td><a href=\'DFrequency.txt\'>Download</a></td></tr>" >> $outputFile\n+fi\n+echo "<tr><td>The dataset used to generate the relative frequency of J gene usage graph</td><td><a href=\'JFrequency.txt\'>Download</a></td></tr>" >> $outputFile\n+echo "<tr><td>The dataset used to generate the relative frequency of the D reading frame graph</td><td><a href=\'DReadingFrame.txt\'>Download</a></td></tr>" >> $outputFile\n+\n+echo "<tr><td colspan=\'2\' style=\'background-color:#E0E0E0;\'>CDR3 Characteristics</td></tr>" >> $outputFile\n+echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href=\'CDR3LengthPlot.txt\'>Download</a></td></tr>" >> $outputFile\n+echo "<tr><td>The dataset used to generate the Amino Acid Composition in the CDR3 graph</td><td><a href=\'AAComposition.txt\'>Download</a></td></tr>" >> $outputFile\n+\n+echo "<tr><td colspan=\'2\' style=\'background-color:#E0E0E0;\'>Heatmaps</td></tr>" >> $outputFile\n+for sample in $samples; do\n+\tif [[ "$useD" == "true" ]] ; then\n+\t\techo "<tr><td>The data used to generate the VD heatmap for $sample.</td><td><a href=\'HeatmapVD_$sample.txt\'>Download</a></td></tr>" >> $outputFile\n+\tfi\n+\techo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href=\'HeatmapVJ_$sample.txt\'>Download</a></td></tr>" >> $outputFile\n+\tif [[ "$useD" == "true" ]] ; then\n+\t\techo "<tr><td>The data used to generate the DJ heatmap for $sample.</td><td><a href=\'HeatmapDJ_$sample.txt\'>Download</a></td></tr>" >> $outputFile\n+\tfi\n+done\n+\n+echo "<tr><td colspan=\'2\' style=\'background-color:#E0E0E0;\'>Circos</td></tr>" >> $outputFile\n+for sample in $samples; do\n+\tif [[ "$useD" == "true" ]] ; then\n+\t\techo "<tr><td>The data used to generate the VD Circos plots for $sample.</td><td><a href=\'${sample}_VD_circos.txt\'>Download</a></td></tr>" >> $outputFile\n+\tfi\n+\techo "<tr><td>The data used to generate the VJ Circos plots for $sample.</td><td><a href=\'${sample}_VJ_circos.txt\'>Download</a></td></tr>" >> $outputFile\n+\tif [[ "$useD" == "true" ]] ; then\n+\t\techo "<tr><td>The data used to generate the DJ Circos plots for $sample.</td><td><a href=\'${sample}_DJ_circos.txt\'>Download</a></td></tr>" >> $outputFile\n+\tfi\n+done\n+\n+#echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href=\'VJCDR3_count.txt\'>Download</a></td></tr>" >> $outputFile\n+\n+echo "<tr><td colspan=\'2\' style=\'background-color:#E0E0E0;\'>Clonality</td></tr>" >> $outputFile\n+echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href=\'clonalityComplete.txt\'>Download</a></td></tr>" >> $outputFile\n+# echo "<tr><td>Sequences that are present in more than one replicate</td><td><a href=\'clonaltypes_replicates.txt\'>Download</a></td></tr>" >> $outputFile\n+\n+echo "</table>" >> $outputFile\n+\n+cat $dir/naive_downloads.htm >> $outputFile\n+\n+echo "</div></html>" >> $outputFile\n' |