Mercurial > repos > davidvanzessen > mutation_analysis
diff wrapper.sh @ 0:8a5a2abbb870 draft default tip
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| author | davidvanzessen |
|---|---|
| date | Mon, 29 Aug 2016 05:36:10 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wrapper.sh Mon Aug 29 05:36:10 2016 -0400 @@ -0,0 +1,603 @@ +#!/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_ca=$9 +naive_output_cg=${10} +naive_output_cm=${11} +filter_unique=${12} +class_filter=${13} +empty_region_filter=${14} +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 +fi + +cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt +cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.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 "10_*"` > $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: ${BLASTN_DIR}" +fi + +echo "---------------- identification ($method) ----------------" +echo "---------------- identification ($method) ----------------<br />" >> $log + +if [[ "${method}" == "custom" ]] ; then + python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt +else + echo "---------------- summary_to_fasta.py ----------------" + echo "---------------- summary_to_fasta.py ----------------<br />" >> $log + + python $dir/summary_to_fasta.py --input $PWD/summary.txt --fasta $PWD/sequences.fasta + + echo -e "qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore" > $outdir/identified_genes.txt + ${BLASTN_DIR}/blastn -task blastn -db $dir/subclass_definition.db -query $PWD/sequences.fasta -outfmt 6 >> $outdir/identified_genes.txt +fi + +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 $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1 + +echo "---------------- creating new IMGT zip ----------------" +echo "---------------- creating new IMGT zip ----------------<br />" >> $log + +mkdir $outdir/new_IMGT + +cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt" +cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt" +cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt" +cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt" +cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt" +cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt" +cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt" +cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt" +cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt" +cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt" + +mkdir $outdir/new_IMGT_ca +cp $outdir/new_IMGT/* $outdir/new_IMGT_ca + +mkdir $outdir/new_IMGT_ca1 +cp $outdir/new_IMGT/* $outdir/new_IMGT_ca1 + +mkdir $outdir/new_IMGT_ca2 +cp $outdir/new_IMGT/* $outdir/new_IMGT_ca2 + +mkdir $outdir/new_IMGT_cg +cp $outdir/new_IMGT/* $outdir/new_IMGT_cg + +mkdir $outdir/new_IMGT_cg1 +cp $outdir/new_IMGT/* $outdir/new_IMGT_cg1 + +mkdir $outdir/new_IMGT_cg2 +cp $outdir/new_IMGT/* $outdir/new_IMGT_cg2 + +mkdir $outdir/new_IMGT_cg3 +cp $outdir/new_IMGT/* $outdir/new_IMGT_cg3 + +mkdir $outdir/new_IMGT_cg4 +cp $outdir/new_IMGT/* $outdir/new_IMGT_cg4 + +mkdir $outdir/new_IMGT_cm +cp $outdir/new_IMGT/* $outdir/new_IMGT_cm + +Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1 + +Rscript $dir/new_imgt.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca" 2>&1 +Rscript $dir/new_imgt.r $outdir/new_IMGT_ca1/ $outdir/merged.txt "ca1" 2>&1 +Rscript $dir/new_imgt.r $outdir/new_IMGT_ca2/ $outdir/merged.txt "ca2" 2>&1 + +Rscript $dir/new_imgt.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg" 2>&1 +Rscript $dir/new_imgt.r $outdir/new_IMGT_cg1/ $outdir/merged.txt "cg1" 2>&1 +Rscript $dir/new_imgt.r $outdir/new_IMGT_cg2/ $outdir/merged.txt "cg2" 2>&1 +Rscript $dir/new_imgt.r $outdir/new_IMGT_cg3/ $outdir/merged.txt "cg3" 2>&1 +Rscript $dir/new_imgt.r $outdir/new_IMGT_cg4/ $outdir/merged.txt "cg4" 2>&1 + +Rscript $dir/new_imgt.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm" 2>&1 + + +tmp="$PWD" +cd $outdir/new_IMGT/ #tar weirdness... +tar -cJf ../new_IMGT.txz * + +cd $outdir/new_IMGT_ca/ +tar -cJf ../new_IMGT_ca.txz * + +cd $outdir/new_IMGT_ca1/ +tar -cJf ../new_IMGT_ca1.txz * + +cd $outdir/new_IMGT_ca2/ +tar -cJf ../new_IMGT_ca2.txz * + +cd $outdir/new_IMGT_cg/ +tar -cJf ../new_IMGT_cg.txz * + +cd $outdir/new_IMGT_cg1/ +tar -cJf ../new_IMGT_cg1.txz * + +cd $outdir/new_IMGT_cg2/ +tar -cJf ../new_IMGT_cg2.txz * + +cd $outdir/new_IMGT_cg3/ +tar -cJf ../new_IMGT_cg3.txz * + +cd $outdir/new_IMGT_cg4/ +tar -cJf ../new_IMGT_cg4.txz * + +cd $outdir/new_IMGT_cm/ +tar -cJf ../new_IMGT_cm.txz * + +cd $tmp + +echo "---------------- mutation_analysis.r ----------------" +echo "---------------- mutation_analysis.r ----------------<br />" >> $log + +classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched" +echo "R mutation analysis" +Rscript $dir/mutation_analysis.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1 + + +echo "---------------- mutation_analysis.py ----------------" +echo "---------------- mutation_analysis.py ----------------<br />" >> $log + +python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --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 "ca,cg,cm" $outdir/ 2>&1 +if [ -e "$outdir/aa_histogram_.png" ]; then + mv $outdir/aa_histogram_.png $outdir/aa_histogram.png + mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt +fi + +genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) + +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 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'>" >> $output + +for func in ${funcs[@]} +do + + echo "---------------- $func table ----------------" + echo "---------------- $func table ----------------<br />" >> $log + + cat $outdir/mutations_${func}.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/plot1 $outdir/plot2 $outdir/plot3 2>&1 + + echo "<table class='pure-table pure-table-striped'>" >> $output + echo "<thead><tr><th>info</th>" >> $output + 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>" >> $output + + while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz + do + if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh + echo "<tr><td>$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} (${cmz})</td><td>${allx}/${ally} (${allz})</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} (${cmz}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output + fi + done < $outdir/data_${func}.txt + echo "</table>" >> $output + #echo "<a href='data_${func}.txt'>Download data</a>" >> $output +done + +echo "<img src='plot1.png' /><br />" >> $output +echo "<img src='plot2.png' /><br />" >> $output +echo "<img src='plot3.png' /><br />" >> $output + +echo "</div>" >> $output #SHM overview tab end + +echo "---------------- images ----------------" +echo "---------------- images ----------------<br />" >> $log + +echo "<div class='tabbertab' title='SHM Frequency'>" >> $output + +if [ -a $outdir/scatter.png ] +then + echo "<img src='scatter.png'/><br />" >> $output + echo "<a href='scatter.txt'>download data</a><br />" >> $output +fi +if [ -a $outdir/frequency_ranges.png ] +then + echo "<img src='frequency_ranges.png'/><br />" >> $output + echo "<a href='frequency_ranges_classes.txt'>download class data</a><br />" >> $output + echo "<a href='frequency_ranges_subclasses.txt'>download subclass data</a><br />" >> $output +fi + +echo "</div>" >> $output #SHM frequency tab end + +echo "<div class='tabbertab' title='Transition tables'>" >> $output + +echo "<table border='0'>" >> $output + +for gene in ${genes[@]} +do + echo "<tr>" >> $output + echo "<td><h1>${gene}</h1></td>" >> $output + echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output + echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output + echo "<td><table class='pure-table transition-table pure-table-bordered'>" >> $output + while IFS=, read from a c g t + do + echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output + 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><img src='transitions_heatmap_all.png' /></td>" >> $output +echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output +echo "<td><table class='pure-table transition-table pure-table-bordered'>" >> $output +while IFS=, read from a c g t + do + echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output +done < $outdir/transitions_all_sum.txt +echo "</table></td>" >> $output + +echo "</tr>" >> $output + +echo "</table>" >> $output + +echo "</div>" >> $output #transition tables tab end + +echo "<div class='tabbertab' title='Antigen Selection'>" >> $output + +if [ -a $outdir/aa_histogram.png ] +then + echo "<img src='aa_histogram.png'/><br />" >> $output + echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output + echo "<img src='aa_histogram_ca.png'/><br />" >> $output + echo "<a href='aa_histogram_ca.txt'>download data</a><br />" >> $output + echo "<img src='aa_histogram_cg.png'/><br />" >> $output + echo "<a href='aa_histogram_cg.txt'>download data</a><br />" >> $output + echo "<img src='aa_histogram_cm.png'/><br />" >> $output + echo "<a href='aa_histogram_cm.txt'>download data</a><br />" >> $output +fi + +echo "<embed src='baseline_ca.pdf' width='700px' height='1000px'>" >> $output +echo "<embed src='baseline_cg.pdf' width='700px' height='1000px'>" >> $output +echo "<embed src='baseline_cm.pdf' width='700px' height='1000px'>" >> $output + +echo "</div>" >> $output #antigen selection tab end + +echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab + +if [ -a $outdir/ca.png ] +then + echo "<img src='ca.png'/><br />" >> $output + echo "<a href='ca.txt'>download data</a><br />" >> $output +fi +if [ -a $outdir/cg.png ] +then + echo "<img src='cg.png'/><br />" >> $output + echo "<a href='cg.txt'>download data</a><br />" >> $output +fi + +echo "</div>" >> $output #CSR tab end + +echo "---------------- change-o MakeDB ----------------" + +mkdir $outdir/change_o + +tmp="$PWD" + +cd $outdir/change_o + +bash $dir/change_o/makedb.sh $input 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/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_ca/1_Summary.txt) -gt "1" ]]; then + bash $dir/change_o/makedb.sh $outdir/new_IMGT_ca.txz false false false $outdir/change_o/change-o-db-ca.txt + bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-ca.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-ca.txt $outdir/change_o/change-o-defined_clones-summary-ca.txt +else + echo "No ca sequences" > "$outdir/change_o/change-o-db-defined_clones-ca.txt" + echo "No ca sequences" > "$outdir/change_o/change-o-defined_clones-summary-ca.txt" +fi + +if [[ $(wc -l < $outdir/new_IMGT_cg/1_Summary.txt) -gt "1" ]]; then + bash $dir/change_o/makedb.sh $outdir/new_IMGT_cg.txz false false false $outdir/change_o/change-o-db-cg.txt + bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-cg.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-cg.txt $outdir/change_o/change-o-defined_clones-summary-cg.txt +else + echo "No cg sequences" > "$outdir/change_o/change-o-db-defined_clones-cg.txt" + echo "No cg sequences" > "$outdir/change_o/change-o-defined_clones-summary-cg.txt" +fi + +if [[ $(wc -l < $outdir/new_IMGT_cm/1_Summary.txt) -gt "1" ]]; then + bash $dir/change_o/makedb.sh $outdir/new_IMGT_cm.txz false false false $outdir/change_o/change-o-db-cm.txt + bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-cm.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-cm.txt $outdir/change_o/change-o-defined_clones-summary-cm.txt +else + echo "No cm sequences" > "$outdir/change_o/change-o-db-defined_clones-cm.txt" + echo "No cm sequences" > "$outdir/change_o/change-o-defined_clones-summary-cm.txt" +fi + +PWD="$tmp" + +echo "<div class='tabbertab' title='Clonality'>" >> $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='Ca'>" >> $output +clonality_table $outdir/change_o/change-o-defined_clones-summary-ca.txt $output +echo "</div>" >> $output + +echo "<div class='tabbertab' title='Cg'>" >> $output +clonality_table $outdir/change_o/change-o-defined_clones-summary-cg.txt $output +echo "</div>" >> $output + +echo "<div class='tabbertab' title='Cm'>" >> $output +clonality_table $outdir/change_o/change-o-defined_clones-summary-cm.txt $output +echo "</div>" >> $output + +echo "</div>" >> $output #clonality tabber end + +echo "</div>" >> $output #clonality tab end + +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</a></td></tr>" >> $output +echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>The data used to generate the first SHM Overview plot</td><td><a href='plot1.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>The data used to generate the sexond SHM Overview plot</td><td><a href='plot2.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>The data used to generate the third SHM Overview plot</td><td><a href='plot3.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output + +echo "<tr><td>Motif data per sequence ID</td><td><a href='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</a></td></tr>" >> $output +echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</td><td><a href='sequence_overview/index.html'>Download</a></td></tr>" >> $output + +echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>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</a></td></tr>" >> $output +echo "<tr><td>Baseline data</td><td><a href='baseline.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf'>Download</a></td></tr>" >> $output +echo "<tr><td>Baseline ca data</td><td><a href='baseline_ca.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>Baseline cg PDF</td><td><a href='baseline_cg.pdf'>Download</a></td></tr>" >> $output +echo "<tr><td>Baseline cg data</td><td><a href='baseline_cg.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>Baseline cm PDF</td><td><a href='baseline_cm.pdf'>Download</a></td></tr>" >> $output +echo "<tr><td>Baseline cm data</td><td><a href='baseline_cm.txt'>Download</a></td></tr>" >> $output + +echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz'>Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered ca sequences</td><td><a href='new_IMGT_ca.txz'>Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered ca1 sequences</td><td><a href='new_IMGT_ca1.txz'>Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered ca2 sequences</td><td><a href='new_IMGT_ca2.txz'>Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered cg sequences</td><td><a href='new_IMGT_cg.txz'>Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered cg1 sequences</td><td><a href='new_IMGT_cg1.txz'>Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered cg2 sequences</td><td><a href='new_IMGT_cg2.txz'>Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered cg3 sequences</td><td><a href='new_IMGT_cg3.txz'>Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered cg4 sequences</td><td><a href='new_IMGT_cg4.txz'>Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered cm sequences</td><td><a href='new_IMGT_cm.txz'>Download</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</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</a></td></tr>" >> $output +echo "<tr><td>The Change-O DB file with defined clones of ca</td><td><a href='change_o/change-o-db-defined_clones-ca.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>The Change-O DB defined clones summary file of ca</td><td><a href='change_o/change-o-defined_clones-summary-ca.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>The Change-O DB file with defined clones of cg</td><td><a href='change_o/change-o-db-defined_clones-cg.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>The Change-O DB defined clones summary file of cg</td><td><a href='change_o/change-o-defined_clones-summary-cg.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>The Change-O DB file with defined clones of cm</td><td><a href='change_o/change-o-db-defined_clones-cm.txt'>Download</a></td></tr>" >> $output +echo "<tr><td>The Change-O DB defined clones summary file of cm</td><td><a href='change_o/change-o-defined_clones-summary-cm.txt'>Download</a></td></tr>" >> $output + +echo "</table>" >> $output + +echo "</div>" >> $output #downloads tab end + +echo "</div>" >> $output #tabs end + +echo "</html>" >> $output + +echo "---------------- baseline ----------------" +echo "---------------- baseline ----------------<br />" >> $log +tmp="$PWD" + +mkdir $outdir/baseline + + +mkdir $outdir/baseline/ca_cg_cm +if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then + cd $outdir/baseline/ca_cg_cm + bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "ca_cg_cm" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt" +else + echo "No sequences" > "$outdir/baseline.txt" +fi + +mkdir $outdir/baseline/ca +if [[ $(wc -l < $outdir/new_IMGT_ca/1_Summary.txt) -gt "1" ]]; then + cd $outdir/baseline/ca + bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_ca.txz "ca" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_ca.pdf" "Sequence.ID" "$outdir/baseline_ca.txt" +else + echo "No ca sequences" > "$outdir/baseline_ca.txt" +fi + +mkdir $outdir/baseline/cg +if [[ $(wc -l < $outdir/new_IMGT_cg/1_Summary.txt) -gt "1" ]]; then + cd $outdir/baseline/cg + bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cg.txz "cg" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cg.pdf" "Sequence.ID" "$outdir/baseline_cg.txt" +else + echo "No cg sequences" > "$outdir/baseline_cg.txt" +fi + +mkdir $outdir/baseline/cm +if [[ $(wc -l < $outdir/new_IMGT_cm/1_Summary.txt) -gt "1" ]]; then + cd $outdir/baseline/cm + bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cm.txz "cm" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cm.pdf" "Sequence.ID" "$outdir/baseline_cm.txt" +else + echo "No cm sequences" > "$outdir/baseline_cm.txt" +fi + +cd $tmp + +echo "---------------- naive_output.r ----------------" +echo "---------------- naive_output.r ----------------<br />" >> $log + +if [[ "$naive_output" != "None" ]] +then + cp $outdir/new_IMGT_ca.txz ${naive_output_ca} + cp $outdir/new_IMGT_cg.txz ${naive_output_cg} + cp $outdir/new_IMGT_cm.txz ${naive_output_cm} +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 border></center></html>" >> $log + +IFS="$tIFS" + + +echo "---------------- Done! ----------------" +echo "---------------- Done! ----------------<br />" >> $outdir/log.html + + + + + + + + + + + + + + + + + + + + +