Mercurial > repos > davidvanzessen > mutation_analysis

diff wrapper.sh @ 53:7290a88ea202 draft

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Uploaded
author davidvanzessen
date Mon, 29 Feb 2016 10:49:39 -0500
parents d3542f87a304
children d8daf8ed39e1
line wrap: on
line diff
--- a/wrapper.sh	Fri Jan 29 08:11:31 2016 -0500
+++ b/wrapper.sh	Mon Feb 29 10:49:39 2016 -0500
@@ -33,6 +33,8 @@
 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
 cat $PWD/files/*/10_* > $PWD/hotspots.txt
 
+cp $dir/tabber.js $outdir
+
 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
 
 echo "${BLASTN_DIR}"
@@ -63,36 +65,54 @@
 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
 echo "R mutation analysis"
 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
+
+#echo "." > $output
+#exit 0
+
 echo "python mutation analysis"
 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
 echo "R AA histogram"
 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1
-cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt
 
 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
 
+funcs=(sum mean median)
 
-echo "<html><center><h1>$title</h1></center><table border='1'>" > $output
-echo "<tr><th>info</th>" >> $output
-for gene in ${genes[@]}
+
+echo "<html><center><h1>$title</h1></center>" >> $output
+
+for func in ${funcs[@]}
 do
-	tmp=`cat $outdir/${gene}_n.txt`
-	echo "<th><a href='matched_${gene}.txt'>${gene} (N = $tmp)</a></th>" >> $output
-done
-tmp=`cat $outdir/total_n.txt`
-echo "<th><a href='matched_all.txt'>all (N = $tmp)</a></th>" >> $output
+	cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/result.txt
+
+	echo "<table border='1' width='100%'><caption><h3>${func} table</h3></caption>" >> $output
+	echo "<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.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 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></tr>" >> $output
-	fi
-done < $outdir/result.txt
+	while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz allx ally allz
+	do
+		if [ "$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></tr>" >> $output
+		fi
+	done < $outdir/result.txt
+
+done
+
 echo "</table>" >> $output
-echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br /><a href='merged.txt'>all data</a><br /><a href='mutation_by_id.txt'>mutations by id</a><br /><a href='aa_id_mutations.txt'>AA mutations location by id</a><br /><a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output
-
+echo "<a href='unmatched.txt'>unmatched</a><br />" >> $output
+echo "<a href='motif_per_seq.txt'>motif per sequence</a><br />" >> $output
+echo "<a href='merged.txt'>all data</a><br />" >> $output
+echo "<a href='mutation_by_id.txt'>mutations by id</a><br />" >> $output
+echo "<a href='aa_id_mutations.txt'>AA mutations location by id</a><br />" >> $output
+echo "<a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output
 
 echo "<img src='all.png'/><br />" >> $output
 echo "<a href='all.txt'>download data</a><br />" >> $output
@@ -129,7 +149,7 @@
 	while IFS=, read from a c g t
 		do
 			echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
-	done < $outdir/transitions_${gene}.txt
+	done < $outdir/transitions_${gene}_sum.txt
 	echo "</table>" >> $output
 done
 
@@ -137,7 +157,7 @@
 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.txt
+done < $outdir/transitions_all_sum.txt
 echo "</table>" >> $output
 
 echo "</html>" >> $output