First version of the scripts for building the CAU tRNA database

Former-commit-id: 443a0446133850bb57211c27d2001241b03472bd
Former-commit-id: 8af464a0786f81dddf795f0cbda9ada9974808bf

detectors/trna/tools/buildCAURefDB.sh

@@ -0,0 +1,124 @@
+#!/bin/bash
+#
+#                           BUILD REFERENCE THE CAU TRNA LIBRARy
+#
+#========================================================================================
+
+# -- CAUTION -- Works as long than the script 
+#               is not called through a symlink
+SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
+source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
+
+function fasta1li {
+
+    awk '/^>/ {if (sequence) \
+                  {print sequence}; \
+               print $0; \
+               sequence=""} \
+         !/^>/ {sequence = sequence $0} \
+         END {print sequence}' $1
+}
+
+function dereplicate {
+	DATA=$1
+	sumaclust -t 1 $DATA | \
+		fasta1li | \
+		grep -A 1 '^>' | \
+		grep -A1 'cluster_center=True;' | \
+		grep -v -- -- | \
+		sed -E "s/count=[0-9]+; //" | \
+		sed 's/cluster_weight/count/' | \
+		awk ' /^>/ {SEQ++;$1=$1"_"SEQ;print $0} \
+			 !/^>/ {print $0}'
+}
+
+function extractSeqs {
+	rm -f $$.index
+	fastaindex -f $1 \
+	           -i $$.index
+	
+	for id in `cat $2`; do
+		fastafetch -f $1 \
+				   -i $$.index \
+				   -q $id 
+	done
+	
+	rm -f $$.index
+}
+
+function goodtrna {
+    local QUERY=$1
+    local REF=$2
+	sumatra -t 0.90 -x $QUERY $REF | \
+		sed -E 's/.(trn.M?)[_A-Z0-9]+/ \1 /' | \
+		sort -k 1,2 | \
+		awk '(OLD) && ($1!=OLD) {print OLD,c["trnM"],c["trnfM"],c["trnI"]} \
+		     (OLD !=$1)         {c["trnM"]=0;c["trnfM"]=0;c["trnI"]=0;OLD=$1} \
+		                        {c[$2]+=$5}' | awk '{p=0;} \
+		     ($2 > $3) && ($2 > $4) { print $0,"trnM";p=1 } \
+		     ($3 > $2) && ($3 > $4) {print $0,"trnfM";p=1} \
+		     ($4 > $2) && ($4 > $3) {print $0,"trnI";p=1} \
+		     (p==0) {print $0,"----"}' |      sed 's/_/ /' | \
+		awk '{print $1"_"$2,$3,$4,$5,$1,$6}' | \
+		awk '(($2+$3+$4) > 1) && ($5==$6) {print $1}'
+}
+
+pushTmpDir ORG.buildSCDB
+
+	CAUFILE=CAU.fasta	
+
+	openLogFile "${TRNA_DATA_DIR}/CAU_tRNA_DB.log"
+	
+	loginfo "Selecting Viridiplantae genebank entries..."
+		VIRIDIPLANTAE=$(${PROG_DIR}/../../normalize/tools/selectViridiplantae.sh $*) 
+		loginfo " --> $(echo ${VIRIDIPLANTAE} | wc -w) entries selected"
+	loginfo "Done"
+	
+	loginfo "Extracting the CAU tRNA from the plants entries..."
+		${PROG_DIR}/extract_refCAUtRNA.sh ${VIRIDIPLANTAE} | \
+			fasta1li | \
+			egrep -A 1 '^>trn(I|M|fM)' | \
+			grep -v -- -- > ${CAUFILE}
+	loginfo "Done"
+
+	loginfo "Sorting the CAU tRNA..."
+	
+		loginfo "Extract and dereplicate trnI..."
+		egrep -A 1 '^>trnI_'  ${CAUFILE} | grep -v -- -- > trnI.fasta
+		dereplicate trnI.fasta > trnCAU.fasta
+		
+		loginfo "Extract and dereplicate trnM..."
+		egrep -A 1 '^>trnM_'  ${CAUFILE} | grep -v -- -- > trnM.fasta
+		dereplicate trnM.fasta >> trnCAU.fasta
+		
+		loginfo "Extract and dereplicate trnfM..."
+		egrep -A 1 '^>trnfM_' ${CAUFILE} | grep -v -- -- > trnfM.fasta
+		dereplicate trnfM.fasta >> trnCAU.fasta
+		
+	loginfo "Done"
+	
+	loginfo "Cleaning the CAU tRNA..."
+
+		loginfo "First pass..."
+		
+		goodtrna 	trnCAU.fasta trnCAU.fasta 	 > trnCAU.good.ids
+		extractSeqs trnCAU.fasta trnCAU.good.ids > trnCAU.good.fasta
+
+		loginfo " --> $(wc -l trnCAU.good.ids) sequences kept"
+		
+		loginfo "Second pass..."
+		
+		goodtrna 	trnCAU.fasta trnCAU.good.fasta > trnCAU.good.ids
+		extractSeqs trnCAU.fasta trnCAU.good.ids   > trnCAU.good.fasta	
+		
+		loginfo " --> $(wc -l trnCAU.good.ids) sequences kept"
+
+	loginfo "Done"
+	
+	loginfo "Installing the CAU tRNA database..."
+		
+		cp trnCAU.good.fasta "${TRNA_DATA_DIR}/CAU_tRNA_DB.fasta"
+
+	loginfo "Done"
+
+popTmpDir