Mercurial > repos > davidvanzessen > mutation_analysis

changeset 126:ffd5462da9d1 draft

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Uploaded
author davidvanzessen
date Mon, 29 Aug 2016 04:20:30 -0400
parents e87dcca14bd6
children afb0937ec0dc
files wrapper.sh
diffstat 1 files changed, 86 insertions(+), 42 deletions(-) [+]
line wrap: on
line diff
--- a/wrapper.sh	Mon Aug 29 03:28:49 2016 -0400
+++ b/wrapper.sh	Mon Aug 29 04:20:30 2016 -0400
@@ -349,7 +349,7 @@
 
 echo "</div>" >> $output #antigen selection tab end
 
-echo "<div class='tabbertab' title='CSR'>" >> $output
+echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
 
 if [ -a $outdir/ca.png ] 
 then
@@ -364,6 +364,91 @@
 
 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
@@ -473,47 +558,6 @@
 
 echo "</table>" >> $outdir/base_overview.html
 
-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"
-
 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