First version of the scripts for building the CAU tRNA database

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

data/trna/CAU_tRNA_DB.log

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+2015-10-10 18:52:35 [OA INFO   ] 63859 -- Selecting Viridiplantae genebank entries...
+2015-10-10 18:52:44 [OA INFO   ] 63859 --  -->      695 entries selected
+2015-10-10 18:52:44 [OA INFO   ] 63859 -- Done
+2015-10-10 18:52:44 [OA INFO   ] 63859 -- Extracting the CAU tRNA from the plants entries...
+2015-10-10 19:03:07 [OA INFO   ] 63859 -- Done
+2015-10-10 19:03:07 [OA INFO   ] 63859 -- Sorting the CAU tRNA...
+2015-10-10 19:03:07 [OA INFO   ] 63859 -- Extract and dereplicate trnI...
+2015-10-10 19:03:07 [OA INFO   ] 63859 -- Extract and dereplicate trnM...
+2015-10-10 19:03:07 [OA INFO   ] 63859 -- Extract and dereplicate trnfM...
+2015-10-10 19:03:07 [OA INFO   ] 63859 -- Done
+2015-10-10 19:03:07 [OA INFO   ] 63859 -- Cleaning the CAU tRNA...
+2015-10-10 19:03:07 [OA INFO   ] 63859 -- First pass...
+2015-10-10 19:03:09 [OA INFO   ] 63859 --  -->      420 trnCAU.good.ids sequences kept
+2015-10-10 19:03:09 [OA INFO   ] 63859 -- Second pass...
+2015-10-10 19:03:11 [OA INFO   ] 63859 --  -->      419 trnCAU.good.ids sequences kept
+2015-10-10 19:03:11 [OA INFO   ] 63859 -- Done
+2015-10-10 19:03:11 [OA INFO   ] 63859 -- Installing the CAU tRNA database...
+2015-10-10 19:03:11 [OA INFO   ] 63859 -- Done

data/trna/ncbi20150303.ndx.REMOVED.git-id

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-0b9d49e3330cd8e6abe0c8b010e9931f7b2f22f3

data/trna/ncbi20150303.tdx.REMOVED.git-id

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-87cabbb1913329a9e693acad81654beb01f0e9bc

detectors/trna/tools/buildCAURefDB.sh

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+#!/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

detectors/trna/tools/extract_refCAUtRNA.sh

@@ -0,0 +1,129 @@
+#!/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 taxid {
+	egrep '/db_xref="taxon:[0-9]+"' $1 | \
+	sed -E 's@ +/db_xref="taxon:([0-9]+)"@\1@'
+}
+
+function ac {
+	head -1 $1 | awk '{print $2}'
+}
+
+function definition {
+	awk '/^DEFINITION/      {on=1}                         \
+	     (on==1)            {printf("%s ",$0)}             \
+	     (/\.$/ && (on==1)) {on=0;print ""}' $1 |          \
+	sed 's/^DEFINITION *//' | \
+	sed 's/ *$//'
+}
+
+function gb2fasta {
+	AC=`ac $1`
+	TAXID=`taxid $1`
+	DEFINITION=`definition $1`
+
+    echo ">${AC} taxid=${TAXID}; ${DEFINITION}"
+    
+    awk '/^\/\//    {on=0}                                             \
+         (on==1)    {print $0}                                         \
+         /^ORIGIN / {on=1}' $1 |                                       \
+    sed -E 's/^ *[0-9]+ +//'   |                                       \
+    sed 's/ //g'
+}
+
+function findCAUtrna {
+
+	FASTATMP="$$.genome.fasta"
+
+	gb2fasta $1 > ${FASTATMP}
+	aragorn -i -w -seq ${FASTATMP} |                               \
+	awk '(on==1) && /^ *[0-9]+/ {on=0;print ""}                       \
+	     (on==1)                {printf($0)}                          \
+	     /\(cat\)$/             {on=1; printf("%s ",$0)}              \
+	     END {print ""}' | \
+	awk '{print $3,$6}'  | \
+	sed -E 's/c?\[([0-9]+),([0-9]+)\]/\1 \2/' | \
+	sed 's/ /:/g'
+	
+	rm ${FASTATMP}
+}
+
+function trnaAnnotations {
+    awk '/^ORIGIN/    {on=0} \
+         (on==1)      {print $0} \
+         /^FEATURE/   {on=1}' $1 | \
+    awk '/^     [^ ]/ {print ""} \
+                      {printf("%s ",$0)} \
+         END          {print ""}' | \
+    sed 's/^ *//' | \
+    sed -E 's/ +/ /g' | \
+    grep '^tRNA' | grep '/gene="' | \
+    sed -E 's/([0-9]+)\.\.([0-9]+)/\1 \2/g' | \
+    sed -E 's/ [0-9]+,[0-9]+ / /g' | \
+    grep -v '>' | \
+    grep -v '<' | \
+    sed -E 's/join\(([0-9]+ [0-9]+)\)/\1/' | \
+    sed -E 's/complement\(([0-9]+ [0-9]+)\)/\1/' | \
+    sed -E 's/join\(([0-9]+ [0-9]+)\)/\1/' | \
+    sed 's/^tRNA *//' |  \
+    sed -E 's@([0-9]+) +([0-9]+).*/gene="([^"]+)"@\1 \2 \3@' | \
+    awk '{print $1,$2,$3}' 
+}
+
+function annotateCAU {
+    DISTTMP="$$.trna.dist"
+	trna=(`echo $1 | sed 's/:/ /g'`) 
+	awk -v b=${trna[0]} -v e=${trna[1]} \
+	    '{printf("sqrt((%d - %d)^2 + (%d - %d)^2)\n",$1,b,$2,e)}' $2 | \
+	bc -l | \
+	sed 's/\..*$//' > ${DISTTMP}
+	paste ${DISTTMP} $2 | sort -nk 1 | head -1 | awk '{print $1,$4}'
+	rm -f ${DISTTMP}
+}
+
+function writeTRNA {
+	TAXID=`taxid $1`	
+	AC=`ac $1`
+	DEFINITION=`definition $1`
+
+	TRNATMP="$$.trna.txt"
+
+	trnaAnnotations $1 > ${TRNATMP}
+	ntrna=`wc -l ${TRNATMP} | awk '{print $1}'`
+
+	if (( ntrna > 0 )); then 
+		trnacau=`findCAUtrna $1`
+
+		for t in $trnacau; do
+			AA=(`annotateCAU $t ${TRNATMP}`)
+			distance=${AA[0]}
+			aa=`echo ${AA[1]} | sed -E 's/(t(rn|RNA)-?)?(I|M|fM).*$/trn\3/'`
+		
+			if (( distance <= 10 )); then
+				echo ">${aa}_${AC} gbac=${AC}; trna=${aa}; taxid=${TAXID}; distance=${distance}; ${DEFINITION}"
+				echo "$t" | awk -F ':' '{print $3}' 
+			fi
+		done
+	fi
+
+	rm -f ${TRNATMP}
+}
+
+pushTmpDir ORG.buildCAUtRNA
+	
+	for gb in $*; do
+		writeTRNA $gb
+	done
+
+popTmpDir
+
+

detectors/trna/tools/reannoteCAURefDB.sh

@@ -1,24 +0,0 @@
-#!/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

scripts/bash_init.sh

@@ -142,6 +142,9 @@ CALL_DIR="$(getAbsolutePath $(pwd))"            # Directory from where the main
 IR_DATA_DIR="${DATA_DIR}/ir"  				  	# Directory containing data related to the 
 												# Inverted repeat strucuture
 								
+TRNA_DATA_DIR="${DATA_DIR}/trna"  				# Directory containing data related to the 
+												# Inverted repeat strucuture
+								
 
 #
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