Initial commit of ORG.Annotate

Former-commit-id: 8c4c1d0391ad06ed67e748e0f837399e9b3de7ad
Former-commit-id: 5af9ed909a6f6bed7bae86c77bd770ae4b5fc14e

annotate_plastid.sh

@@ -0,0 +1,96 @@
+#!/bin/bash
+#
+#
+
+export ORGANNOT_HOME=`dirname $0`
+
+REPSEEK=${ORGANNOT_HOME}/repseek
+SUMATRA=${ORGANNOT_HOME}/sumatra
+ARAGORN=${ORGANNOT_HOME}/aragorn
+WRAPARAGORN=${ORGANNOT_HOME}/aragorn_wrapper.awk
+ECOFIND=${ORGANNOT_HOME}/ecofind
+
+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}
+}
+
+function gffTRNA {
+
+	${ARAGORN} -w -io -seq $3 | awk -v gid=${1} -f ${WRAPARAGORN}
+
+}
+
+# s'alimente avec un fichier.fasta
+# $3 : nb de caractere du fichier, t : nb de caractere du titre,
+# $1+1 : nb de retour chariot du fichier
+function seqlength {
+  cat $1 | \
+  wc |\
+  awk -v t="`head -1 $1 | wc -c`" '{print $3 - t - $1 + 1}'
+}
+
+
+# recupere les informations issues du programme repseek avec l'origine des deux
+# IR et leur taille
+function lookforIR {
+	${REPSEEK} -c -p 0.001 $1 |                                     \
+     grep 'Distant.inv'       |                                     \
+     sort -n -k4              |                                     \
+     tail -1                  |                                     \
+     awk '{print $7}'         |                                     \
+     sed 's/-/ /g'
+}
+
+# recupere le nom de la sequence analyse
+function seqName {
+		 head -n1 $1|                                                          \
+	     awk '{print $1}' |                                                    \
+	     sed 's/^>//' |                                                        \
+	     sed -E 's/.*\|([^|]+)\|/\1/'
+}
+
+# cree un resume du fichier analyse au format gff
+# ex : GFF (NC_***	Repseek	IR1 start	end .	+	.	)
+function gffIR {
+	lseq=$2
+	nom=$1
+    lookforIR $3 |                                                             \
+    awk -v nom="$nom" -v  lseq="$lseq"                                         \
+    	'BEGIN {OFS="\t"}                                                      \
+    	{  startIR1=$1;                  \
+    	   startIR2=$2; \
+    	   endIR1=startIR1 + $3 -1; \
+    	   endIR2=startIR2 + $3 -1; \
+    	   startSSC=1; \
+    	   endSSC=startIR1-1; \
+    	   startLSC=endIR1+1; \
+    	   endLSC=startIR2-1; \
+    	                \
+    	   print nom,"RepSeek","misc_feature",startSSC,endSSC,"\.","+","\.","ID=SSC;note=small single copy region";\
+    	   print nom,"RepSeek","repeat_region",startIR1,endIR1,"\.","+","\.","ID=IRA;note=inverted repeat A";\
+    	   print nom,"RepSeek","misc_feature",startLSC,endLSC,"\.","+","\.","ID=LSC;note=large single copy region";\
+    	   print nom,"RepSeek","repeat_region",startIR2,endIR2,"\.","-","\.","ID=IRB;note=inverted repeat B";\
+    	}'
+}
+
+
+echo "##gff-version 3"
+
+
+genome=$1
+genome_name=`seqName $1`
+genome_length=`seqlength $1`
+
+gffIR   ${genome_name} ${genome_length} ${genome}| grep -v '^ *$'
+gffTRNA ${genome_name} ${genome_length} ${genome}| grep -v '^ *$'