Add annotation of nuclear rDNA cistron

Former-commit-id: ee54019ddddbea4d17956622968f6ce673b609e1
Former-commit-id: 5e5381cf59409ca3dc01098b0e3f330efe0a6a32

detectors/nucrrna/bin/go_nucrrna.sh

@@ -0,0 +1,88 @@
+#!/bin/bash
+#
+#           Annotate the Intergenic Spacer (ITS) of nuclear rDNA cluster
+#
+#========================================================================================
+#
+# This script is based on ITSx
+# 
+#
+#  go_its.sh <FASTAFILE>
+#
+#		- <FASTAFILE> : The fasta file containing the cluster to annotate
+#
+#  Results are printed to the standart output
+#
+#========================================================================================
+
+# -- CAUTION -- Works as long than the script 
+#               is not called through a symlink
+THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
+source "${THIS_DIR}/../../../scripts/bash_init.sh"
+
+pushTmpDir ORG.its
+
+	loginfo "Annotating ITS and TSU..."
+
+	RRNADB="${NUCRRNA_DATA_DIR}/plants/nuc_RRNA.hmm"
+	
+	if [[ ! "$1" =~ ^/ ]]; then
+		QUERY="${CALL_DIR}/$1"
+	else
+		QUERY="$1"
+	fi
+
+
+    ITSx -p "${ITS_DATA_DIR}/ITSx_db/HMMs" -i "${QUERY}" -o "output.itsx"
+    
+    ITS1=( $(sed -E 's/.*ITS1: *([0-9]+)-([0-9]+).*/\1 \2/' "output.itsx.positions.txt" ) )
+    ITS2=( $(sed -E 's/.*ITS2: *([0-9]+)-([0-9]+).*/\1 \2/' "output.itsx.positions.txt" ) )
+    TSU=( $(sed -E 's/.*5\.8S: *([0-9]+)-([0-9]+).*/\1 \2/' "output.itsx.positions.txt" ) )
+
+
+    
+    if [[ ${#ITS1[@]}=="2" ]]  ; then
+    	echo "FT   misc_RNA        ${ITS1[0]}..${ITS1[1]}"
+		echo 'FT                   /gene="ITS1"'
+		echo 'FT                   /note="internal transcribed spacer 1, ITS1"'
+	fi
+	
+    if [[ ${#TSU[@]}=="2" ]]  ; then
+		echo "FT   rRNA            ${TSU[0]}..${TSU[1]}"
+		echo 'FT                   /gene="5.8S rRNA"'
+		echo 'FT                   /product="5.8S ribosomal nuclear RNA"'
+	fi
+	
+    if [[ ${#ITS2[@]}=="2" ]]  ; then
+		echo "FT   misc_RNA        ${ITS2[0]}..${ITS2[1]}"
+		echo 'FT                   /gene="ITS2"'
+		echo 'FT                   /note="internal transcribed spacer 2, ITS2"'
+	fi
+    
+
+	hmmsearch --max ${RRNADB} ${QUERY} | \
+		$AwkCmd '/Query: / { \
+		                profil=$2; \
+		                match($3,"[0-9][0-9]*");\
+		                lprof=substr($3,RSTART,RLENGTH)} \
+		     / [0-9][0-9]* ! / { \
+		                print profil,lprof,$7,$8,$10,$11}' | \
+		$AwkCmd '($3 <=5) && (($2-$4) <=5) { \
+		                full=1;$5=$5-$3+1;$6=$6+($2-$4)}  \
+		               {loc=$5".."$6} \
+		     ($1 ~ /_RC$/) { \
+		                loc="complement("loc")"} \
+		     (full==1) {match($1,"_..*S");\
+		                rrna=substr($1,RSTART+1,RLENGTH-1);\
+		                print "FT   rRNA            " loc; \
+		                print "FT                   /gene=\"rrn"rrna"\""
+		                print "FT                   /product=\""rrna" ribosomal RNA\"";\
+		                full=0
+		                }'	
+
+    loginfo "Done."
+
+popTmpDir
+
+exit 0
+