Mercurial > repos > davidvanzessen > shm_csr
view wrapper.sh @ 82:a103134ee6e0 draft
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author | davidvanzessen |
---|---|
date | Thu, 25 Feb 2021 10:32:32 +0000 |
parents | b6f9a640e098 |
children | 729738462297 |
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#!/bin/bash #set -e dir="$(cd "$(dirname "$0")" && pwd)" input=$1 method=$2 log=$3 #becomes the main html page at the end outdir=$4 output="$outdir/index.html" #copied to $log location at the end title="$5" include_fr1=$6 functionality=$7 unique=$8 naive_output=$9 naive_output_ca=${10} naive_output_cg=${11} naive_output_cm=${12} naive_output_ce=${13} naive_output_all=${14} filter_unique=${15} filter_unique_count=${16} class_filter=${17} empty_region_filter=${18} fast=${19} mkdir $outdir tar -xzf $dir/style.tar.gz -C $outdir echo "---------------- read parameters ----------------" echo "---------------- read parameters ----------------<br />" > $log echo "unpacking IMGT file" type="`file $input`" if [[ "$type" == *"Zip archive"* ]] ; then echo "Zip archive" echo "unzip $input -d $PWD/files/" unzip $input -d $PWD/files/ elif [[ "$type" == *"XZ compressed data"* ]] ; then echo "ZX archive" echo "tar -xJf $input -C $PWD/files/" mkdir -p "$PWD/files/$title" tar -xJf $input -C "$PWD/files/$title" else echo "Unrecognized format $type" echo "Unrecognized format $type" > $log exit 1 fi cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt cat "`find $PWD/files/ -name "2_*"`" > $PWD/gapped_nt.txt cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt cat "`find $PWD/files/ -name "9_*"`" > $PWD/aa_change_stats.txt cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt echo "---------------- unique id check ----------------" Rscript $dir/check_unique_id.r $PWD/summary.txt $PWD/gapped_nt.txt $PWD/sequences.txt $PWD/gapped_aa.txt $PWD/aa.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/aa_change_stats.txt $PWD/hotspots.txt if [[ ${#BLASTN_DIR} -ge 5 ]] ; then echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}" else BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin" echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}" fi echo "---------------- class identification ----------------" echo "---------------- class identification ----------------<br />" >> $log python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt echo "---------------- merge_and_filter.r ----------------" echo "---------------- merge_and_filter.r ----------------<br />" >> $log Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1 if [[ "${naive_output}" == "yes" ]] || [[ "$fast" == "no" ]] ; then echo "---------------- creating new IMGT zips ----------------" echo "---------------- creating new IMGT zips ----------------<br />" >> $log mkdir $outdir/new_IMGT cp $PWD/summary.txt "$outdir/new_IMGT/1_Summary.txt" cp $PWD/gapped_nt.txt "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt" cp $PWD/sequences.txt "$outdir/new_IMGT/3_Nt-sequences.txt" cp $PWD/gapped_aa.txt "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt" cp $PWD/aa.txt "$outdir/new_IMGT/5_AA-sequences.txt" cp $PWD/junction.txt "$outdir/new_IMGT/6_Junction.txt" cp $PWD/mutationanalysis.txt "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt" cp $PWD/mutationstats.txt "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt" cp $PWD/aa_change_stats.txt "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt" cp $PWD/hotspots.txt "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt" mkdir $outdir/new_IMGT_IGA cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA mkdir $outdir/new_IMGT_IGA1 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1 mkdir $outdir/new_IMGT_IGA2 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2 mkdir $outdir/new_IMGT_IGG cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG mkdir $outdir/new_IMGT_IGG1 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1 mkdir $outdir/new_IMGT_IGG2 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2 mkdir $outdir/new_IMGT_IGG3 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3 mkdir $outdir/new_IMGT_IGG4 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4 mkdir $outdir/new_IMGT_IGM cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM mkdir $outdir/new_IMGT_IGE cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1 tmp="$PWD" cd $outdir/new_IMGT/ #tar weirdness... tar -cJf ../new_IMGT.txz * cd $outdir/new_IMGT_IGA/ tar -cJf ../new_IMGT_IGA.txz * cd $outdir/new_IMGT_IGA1/ tar -cJf ../new_IMGT_IGA1.txz * cd $outdir/new_IMGT_IGA2/ tar -cJf ../new_IMGT_IGA2.txz * cd $outdir/new_IMGT_IGG/ tar -cJf ../new_IMGT_IGG.txz * cd $outdir/new_IMGT_IGG1/ tar -cJf ../new_IMGT_IGG1.txz * cd $outdir/new_IMGT_IGG2/ tar -cJf ../new_IMGT_IGG2.txz * cd $outdir/new_IMGT_IGG3/ tar -cJf ../new_IMGT_IGG3.txz * cd $outdir/new_IMGT_IGG4/ tar -cJf ../new_IMGT_IGG4.txz * cd $outdir/new_IMGT_IGM/ tar -cJf ../new_IMGT_IGM.txz * cd $outdir/new_IMGT_IGE/ tar -cJf ../new_IMGT_IGE.txz * cd $tmp fi echo "---------------- shm_csr.r ----------------" echo "---------------- shm_csr.r ----------------<br />" >> $log classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched" echo "R mutation analysis" Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1 echo "---------------- plot_pdfs.r ----------------" echo "---------------- plot_pdfs.r ----------------<br />" >> $log echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1" Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1 echo "---------------- shm_csr.py ----------------" echo "---------------- shm_csr.py ----------------<br />" >> $log python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt echo "---------------- aa_histogram.r ----------------" echo "---------------- aa_histogram.r ----------------<br />" >> $log Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1 if [ -e "$outdir/aa_histogram_.png" ]; then mv $outdir/aa_histogram_.png $outdir/aa_histogram.png mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt fi genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE) funcs=(sum mean median) funcs=(sum) echo "---------------- sequence_overview.r ----------------" echo "---------------- sequence_overview.r ----------------<br />" >> $log mkdir $outdir/sequence_overview Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1 echo "<table border='1'>" > $outdir/base_overview.html while IFS=$'\t' read ID class seq A C G T do echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html done < $outdir/sequence_overview/ntoverview.txt echo "<html><center><h1>$title</h1></center>" > $output echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output echo "<script type='text/javascript' src='tabber.js'></script>" >> $output echo "<script type='text/javascript' src='script.js'></script>" >> $output echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`" unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`" total_count=$((matched_count + unmatched_count)) perc_count=$((unmatched_count / total_count * 100)) perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"` perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"` echo "<center><h2>Total: ${total_count}</h2></center>" >> $output echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output echo "---------------- main tables ----------------" echo "---------------- main tables ----------------<br />" >> $log echo "<div class='tabber'>" >> $output echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output for func in ${funcs[@]} do echo "---------------- $func table ----------------" echo "---------------- $func table ----------------<br />" >> $log cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt echo "---------------- pattern_plots.r ----------------" echo "---------------- pattern_plots.r ----------------<br />" >> $log Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/absolute_mutations $outdir/shm_overview.txt 2>&1 echo "<table class='pure-table pure-table-striped'>" >> $output echo "<thead><tr><th>info</th>" >> $output if [ "${class_filter}" != "101_101" ] ; then for gene in ${genes[@]} do tmp=`cat $outdir/${gene}_${func}_n.txt` echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output done tmp=`cat $outdir/all_${func}_n.txt` echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output tmp=`cat $outdir/unmatched_${func}_n.txt` echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz do if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] || [ "$name" == "Tandems/Expected (ratio)" ] ; then #meh echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${cex}/${cey} (${cez})</td><td>${allx}/${ally} (${allz})</td><td>${unx}/${uny} (${unz})</td></tr>" >> $output elif [ "$name" == "Median of Number of Mutations (%)" ] ; then echo "<tr><td>$name</td><td>${caz}%</td><td>${ca1z}%</td><td>${ca2z}%</td><td>${cgz}%</td><td>${cg1z}%</td><td>${cg2z}%</td><td>${cg3z}%</td><td>${cg4z}%</td><td>${cmz}%</td><td>${cez}%</td><td>${allz}%</td><td>${unz}%</td></tr>" >> $output else echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${cex}/${cey} (${cez}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output fi done < $outdir/data_${func}.txt else tmp=`cat $outdir/all_${func}_n.txt` echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz do if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output elif [ "$name" == "Median of Number of Mutations (%)" ] ; then echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output else echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output fi done < $outdir/data_${func}.txt fi echo "</table>" >> $output #echo "<a href='data_${func}.txt'>Download data</a>" >> $output done echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output echo "<br />" >> $output cat $dir/shm_overview.htm >> $output echo "</div>" >> $output #SHM overview tab end echo "---------------- images ----------------" echo "---------------- images ----------------<br />" >> $log echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output if [ -a $outdir/scatter.png ] then echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output fi if [ -a $outdir/frequency_ranges.png ] then echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output fi echo "<br />" >> $output cat $dir/shm_frequency.htm >> $output echo "</div>" >> $output #SHM frequency tab end echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output echo "<table border='0'>" >> $output for gene in ${genes[@]} do echo "<tr>" >> $output echo "<td><h1>${gene}</h1></td>" >> $output if [ -e $outdir/transitions_heatmap_${gene}.png ] then echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output else echo "<td></td>" >> $output fi if [ -e $outdir/transitions_stacked_${gene}.png ] then echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output else echo "<td></td>" >> $output fi echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output first="true" while IFS=, read from a c g t do if [ "$first" == "true" ] ; then echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output first="false" else echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output fi done < $outdir/transitions_${gene}_sum.txt echo "</table></td>" >> $output echo "</tr>" >> $output done echo "<tr>" >> $output echo "<td><h1>All</h1></td>" >> $output echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output first="true" while IFS=, read from a c g t do if [ "$first" == "true" ] ; then echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output first="false" else echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output fi done < $outdir/transitions_all_sum.txt echo "</table></td>" >> $output echo "</tr>" >> $output echo "</table>" >> $output echo "<br />" >> $output cat $dir/shm_transition.htm >> $output echo "</div>" >> $output #transition tables tab end echo "<div class='tabbertab' title='Antigen Selection'>" >> $output if [ -e $outdir/aa_histogram.png ] then echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output fi if [ -e $outdir/aa_histogram_IGA.png ] then echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output fi if [ -e $outdir/aa_histogram_IGG.png ] then echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output fi if [ -e $outdir/aa_histogram_IGM.png ] then echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output fi if [ -e $outdir/aa_histogram_IGE.png ] then echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output fi if [[ "$fast" == "no" ]] ; then echo "---------------- baseline ----------------" echo "---------------- baseline ----------------<br />" >> $log tmp="$PWD" mkdir $outdir/baseline echo "<center><h1>BASELINe</h1>" >> $output header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)" baseline_boundaries="27:27:38:55:65:104:-" if [[ "${empty_region_filter}" == "leader" ]] ; then baseline_boundaries="1:26:38:55:65:104:-" header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)" fi echo "<p>${header_substring}</p></center>" >> $output mkdir $outdir/baseline/IGA_IGG_IGM if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGA_IGG_IGM bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt" else echo "No sequences" > "$outdir/baseline.txt" fi mkdir $outdir/baseline/IGA if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGA bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt" else echo "No IGA sequences" > "$outdir/baseline_IGA.txt" fi mkdir $outdir/baseline/IGG if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGG bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt" else echo "No IGG sequences" > "$outdir/baseline_IGG.txt" fi mkdir $outdir/baseline/IGM if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGM bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt" else echo "No IGM sequences" > "$outdir/baseline_IGM.txt" fi mkdir $outdir/baseline/IGE if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGE bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt" else echo "No IGE sequences" > "$outdir/baseline_IGE.txt" fi cd $tmp echo "Cleaning up *.RData files" find $outdir/baseline -name "*.RData" -type f -delete if [ -e $outdir/baseline.pdf ] then echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output fi if [ -e $outdir/baseline_IGA.pdf ] then echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output fi if [ -e $outdir/baseline_IGG.pdf ] then echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output fi if [ -e $outdir/baseline_IGM.pdf ] then echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output fi if [ -e $outdir/baseline_IGE.pdf ] then echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output fi fi echo "<br />" >> $output cat $dir/shm_selection.htm >> $output echo "</div>" >> $output #antigen selection tab end echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab if [ -e $outdir/IGA.png ] then echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output fi if [ -e $outdir/IGG.png ] then echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output fi echo "<br />" >> $output cat $dir/shm_csr.htm >> $output echo "</div>" >> $output #CSR tab end if [[ "$fast" == "no" ]] ; then echo "---------------- change-o MakeDB ----------------" mkdir $outdir/change_o tmp="$PWD" cd $outdir/change_o bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-db-defined_first_clones.txt 2>&1 mkdir $outdir/new_IMGT_changeo cp $outdir/new_IMGT/* $outdir/new_IMGT_changeo Rscript $dir/new_imgt.r $outdir/new_IMGT_changeo $outdir/change_o/change-o-db-defined_first_clones.txt "-" 2>&1 cd $outdir/new_IMGT_changeo tar -cJf ../new_IMGT_first_seq_of_clone.txz * cd $outdir/change_o rm -rf $outdir/new_IMGT_changeo Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1" if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGA.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-defined_clones-summary-IGA.txt Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-db-defined_first_clones-IGA.txt 2>&1 mkdir $outdir/new_IMGT_IGA_changeo cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA_changeo Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA_changeo $outdir/change_o/change-o-db-defined_first_clones-IGA.txt "-" 2>&1 cd $outdir/new_IMGT_IGA_changeo tar -cJf ../new_IMGT_IGA_first_seq_of_clone.txz * rm -rf $outdir/new_IMGT_IGA_changeo cd $outdir/change_o else echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt" echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt" fi if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGG.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-defined_clones-summary-IGG.txt Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-db-defined_first_clones-IGG.txt 2>&1 mkdir $outdir/new_IMGT_IGG_changeo cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG_changeo Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG_changeo $outdir/change_o/change-o-db-defined_first_clones-IGG.txt "-" 2>&1 cd $outdir/new_IMGT_IGG_changeo tar -cJf ../new_IMGT_IGG_first_seq_of_clone.txz * rm -rf $outdir/new_IMGT_IGG_changeo cd $outdir/change_o else echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt" echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt" fi if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-db-defined_first_clones-IGM.txt 2>&1 mkdir $outdir/new_IMGT_IGM_changeo cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM_changeo Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM_changeo $outdir/change_o/change-o-db-defined_first_clones-IGM.txt "-" 2>&1 cd $outdir/new_IMGT_IGM_changeo tar -cJf ../new_IMGT_IGM_first_seq_of_clone.txz * rm -rf $outdir/new_IMGT_IGM_changeo cd $outdir/change_o else echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt" echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt" fi if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-db-defined_first_clones-IGE.txt 2>&1 mkdir $outdir/new_IMGT_IGE_changeo cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE_changeo Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE_changeo $outdir/change_o/change-o-db-defined_first_clones-IGE.txt "-" 2>&1 cd $outdir/new_IMGT_IGE_changeo tar -cJf ../new_IMGT_IGE_first_seq_of_clone.txz * rm -rf $outdir/new_IMGT_IGE_changeo cd $outdir/change_o else echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt" echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt" fi cd "$tmp" rm -rf $outdir/new_IMGT rm -rf $outdir/new_IMGT_IGA/ rm -rf $outdir/new_IMGT_IGA1/ rm -rf $outdir/new_IMGT_IGA2/ rm -rf $outdir/new_IMGT_IGG/ rm -rf $outdir/new_IMGT_IGG1/ rm -rf $outdir/new_IMGT_IGG2/ rm -rf $outdir/new_IMGT_IGG3/ rm -rf $outdir/new_IMGT_IGG4/ rm -rf $outdir/new_IMGT_IGM/ rm -rf $outdir/new_IMGT_IGE/ echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab function clonality_table { local infile=$1 local outfile=$2 echo "<table class='pure-table pure-table-striped'>" >> $outfile echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile first='true' while read size clones seqs do if [[ "$first" == "true" ]]; then first="false" continue fi echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile done < $infile echo "</table>" >> $outfile } echo "<div class='tabber'>" >> $output echo "<div class='tabbertab' title='All'>" >> $output clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output echo "</div>" >> $output echo "<div class='tabbertab' title='IGA'>" >> $output clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output echo "</div>" >> $output echo "<div class='tabbertab' title='IGG'>" >> $output clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output echo "</div>" >> $output echo "<div class='tabbertab' title='IGM'>" >> $output clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output echo "</div>" >> $output echo "<div class='tabbertab' title='IGE'>" >> $output clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output echo "</div>" >> $output echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output cat "$outdir/sequence_overview/index.html" | sed -e 's:</td>:</td>\n:g' | sed "s:href='\(.*\).html:href='sequence_overview/\1.html:g" >> $output # rewrite href to 'sequence_overview/..." echo "</div>" >> $output echo "</div>" >> $output #clonality tabber end echo "<br />" >> $output cat $dir/shm_clonality.htm >> $output echo "</div>" >> $output #clonality tab end fi echo "<div class='tabbertab' title='Downloads'>" >> $output echo "<table class='pure-table pure-table-striped'>" >> $output echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='shm_overview.txt' download='shm_overview.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt' download='motif_per_seq.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt' download='mutation_by_id.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='absolute_mutations.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Data about tandem mutations by ID</td><td><a href='tandems_by_id.txt' download='tandems_by_id.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data used to generate the frequency by class plot</td><td><a href='frequency_ranges_classes.txt' download='frequency_ranges_classes.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for frequency by subclass</td><td><a href='frequency_ranges_subclasses.txt' download='frequency_ranges_subclasses.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transitions_all_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_IGA_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGA2' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transitions_IGG_sum.txt' download='transitions_IGG_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transitions_IGG1_sum.txt' download='transitions_IGG1_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transitions_IGG2_sum.txt' download='transitions_IGG2_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transitions_IGG3_sum.txt' download='transitions_IGG3_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transitions_IGG4_sum.txt' download='transitions_IGG4_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transitions_IGM_sum.txt' download='transitions_IGM_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transitions_IGE_sum.txt' download='transitions_IGE_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Presence of AA per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data used to generate the aa mutation frequency plot</td><td><a href='aa_histogram_sum.txt' download='aa_histogram_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data used to generate the aa mutation frequency plot for IGA</td><td><a href='aa_histogram_sum_IGA.txt' download='aa_histogram_sum_IGA.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data used to generate the aa mutation frequency plot for IGG</td><td><a href='aa_histogram_sum_IGG.txt' download='aa_histogram_sum_IGG.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data used to generate the aa mutation frequency plot for IGM</td><td><a href='aa_histogram_sum_IGM.txt' download='aa_histogram_sum_IGM.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data used to generate the aa mutation frequency plot for IGE</td><td><a href='aa_histogram_sum_IGE.txt' download='aa_histogram_sum_IGE.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf' download='baseline.pdf' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output echo "<tr><td>The data for the IGA subclass distribution plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The data for the IGG subclass distribution plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href='change_o/change-o-db-defined_clones.txt' download='change_o/change-o-db-defined_clones.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt' download='change_o/change-o-defined_clones-summary.txt' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just just the first sequence of a clone</td><td><a href='new_IMGT_first_seq_of_clone.txz' download='new_IMGT_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones of IGA</td><td><a href='change_o/change-o-db-defined_clones-IGA.txt' download='change_o/change-o-db-defined_clones-IGA.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGA)</td><td><a href='new_IMGT_IGA_first_seq_of_clone.txz' download='new_IMGT_IGA_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href='change_o/change-o-db-defined_clones-IGG.txt' download='change_o/change-o-db-defined_clones-IGG.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGG)</td><td><a href='new_IMGT_IGG_first_seq_of_clone.txz' download='new_IMGT_IGG_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGM)</td><td><a href='new_IMGT_IGM_first_seq_of_clone.txz' download='new_IMGT_IGM_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones of IGE</td><td><a href='change_o/change-o-db-defined_clones-IGE.txt' download='change_o/change-o-db-defined_clones-IGE.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGE)</td><td><a href='new_IMGT_IGE_first_seq_of_clone.txz' download='new_IMGT_IGE_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='new_IMGT_IGA2.txz' download='new_IMGT_IGA2.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='new_IMGT_IGG.txz' download='new_IMGT_IGG.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='new_IMGT_IGG1.txz' download='new_IMGT_IGG1.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='new_IMGT_IGG2.txz' download='new_IMGT_IGG2.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGE.txz' >Download</a></td></tr>" >> $output echo "</table>" >> $output echo "<br />" >> $output cat $dir/shm_downloads.htm >> $output echo "</div>" >> $output #downloads tab end echo "</div>" >> $output #tabs end echo "</html>" >> $output echo "---------------- naive_output.r ----------------" echo "---------------- naive_output.r ----------------<br />" >> $log if [[ "$naive_output" == "yes" ]] then echo "output naive output" if [[ "${class_filter}" == "101_101" ]] then echo "copy new_IMGT.txz to ${naive_output_all}" cp $outdir/new_IMGT.txz ${naive_output_all} else echo "copy for classes" cp $outdir/new_IMGT_IGA.txz ${naive_output_ca} cp $outdir/new_IMGT_IGG.txz ${naive_output_cg} cp $outdir/new_IMGT_IGM.txz ${naive_output_cm} cp $outdir/new_IMGT_IGE.txz ${naive_output_ce} fi fi echo "</table>" >> $outdir/base_overview.html mv $log $outdir/log.html 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 />" > $log echo "<table border = 1>" >> $log echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log tIFS="$TMP" IFS=$'\t' while read step seq perc do echo "<tr>" >> $log echo "<td>$step</td>" >> $log echo "<td>$seq</td>" >> $log echo "<td>${perc}%</td>" >> $log echo "</tr>" >> $log done < $outdir/filtering_steps.txt echo "</table>" >> $log echo "<br />" >> $log cat $dir/shm_first.htm >> $log echo "</center></html>" >> $log IFS="$tIFS" echo "---------------- Done! ----------------" echo "---------------- Done! ----------------<br />" >> $outdir/log.html