# HG changeset patch
# User davidvanzessen
# Date 1481813057 18000
# Node ID 22fabe161cf38d703207be0c4ed6ceb59bd6df0d
# Parent  4c5ba6b5d10d0badeb6c14b632ba04343cbcc6d0
Uploaded

diff -r 4c5ba6b5d10d -r 22fabe161cf3 sequence_overview.r
--- a/sequence_overview.r	Thu Dec 15 09:21:54 2016 -0500
+++ b/sequence_overview.r	Thu Dec 15 09:44:17 2016 -0500
@@ -245,9 +245,6 @@
 	
 	in.cg.all = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0 & cg4.n > 0)
 	
-	
-	
-	
 	#rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, un.html)
 	rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, ce.html, un.html)
 	rw = c(rw, ca.n, cg.n, cm.n, ce.n, in.classes, in.ca.cg, in.ca.cg.cm, in.ca.cg.ce, in.ca.cg.cm.ce, in.ca1.ca2, in.cg1.cg2, in.cg1.cg3, in.cg1.cg4, in.cg2.cg3, in.cg2.cg4, in.cg3.cg4, in.cg1.cg2.cg3, in.cg2.cg3.cg4, in.cg1.cg2.cg4, in.cg1.cg3.cg4, in.cg.all)
diff -r 4c5ba6b5d10d -r 22fabe161cf3 wrapper.sh
--- a/wrapper.sh	Thu Dec 15 09:21:54 2016 -0500
+++ b/wrapper.sh	Thu Dec 15 09:44:17 2016 -0500
@@ -410,29 +410,85 @@
 fi
 
 
-if [ -e $outdir/baseline.pdf ]
-then
-	echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
-fi
+
+if [[ "$fast" == "no" ]] ; then
+
+	echo "---------------- baseline ----------------"
+	echo "---------------- baseline ----------------<br />" >> $log
+	tmp="$PWD"
+
+	mkdir $outdir/baseline
+
 
-if [ -e $outdir/baseline_IGA.pdf ]
-then
-	echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
-fi
+	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 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$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 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$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 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
+	else
+		echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
+	fi
 
-if [ -e $outdir/baseline_IGG.pdf ]
-then
-	echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
-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 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$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 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$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
 
-if [ -e $outdir/baseline_IGM.pdf ]
-then
-	echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
-fi
+	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_IGE.pdf ]
-then
-	echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
+	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 "</div>" >> $output #antigen selection tab end
@@ -651,62 +707,6 @@
 echo "</html>" >> $output
 
 
-if [[ "$fast" == "no" ]] ; then
-
-	echo "---------------- baseline ----------------"
-	echo "---------------- baseline ----------------<br />" >> $log
-	tmp="$PWD"
-
-	mkdir $outdir/baseline
-
-
-	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 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$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 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$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 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$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 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$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 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$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
-
-fi
-
 echo "---------------- naive_output.r ----------------"
 echo "---------------- naive_output.r ----------------<br />" >> $log