First commit - second part

Former-commit-id: 202296404e6a70f8ae96db99faffb456104c57e9
Former-commit-id: 118417735d2055683607df9809c9b721cc1b1bab

detectors/trna/tools/reannoteCAURefDB.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+SUMATRA=`dirname $0`/sumatra
+
+function annotateCAU {
+	QUERY="$$.query.fasta"
+	echo $1 | sed 's/&/ /' | tr '@' '\n' > ${QUERY}
+	${SUMATRA} -d -n ${QUERY} $2  2> /dev/null | \
+	awk '    {n[$2]+=1;d[$2]+=$3} \
+	     END {for (i in n) \
+	            print i, n[i],d[i], d[i]/n[i]\
+	         }' | \
+	sort -rnk4 | \
+	egrep '^trn(I|M|fM)' | \
+	tail -1 | \
+	awk '{print $1,$NF}'
+	rm -rf ${QUERY}
+}
+
+
+for seq in `awk '(on==1) && /^>/ {print "";on=0} /^>/ {printf("%s@",$0)} ! /^>/ {on=1;printf($0)}' $1 | tr ' ' '&'`; do
+    new=(`annotateCAU ${seq} $1`)
+	echo $seq | sed 's/&/ /g' | sed -E 's/>([^ ]+) />'${new[0]}' /' | tr '@' '\n'
+done