First version of the tRNA detector and of the global organnot.sh script

annotate_plastid.sh

-#!/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} ${genome}| grep -v '^ *$'

detectors/ir/bin/go_ir.sh

@@ -61,4 +61,4 @@ pushTmpDir ORG.ir
 
 popTmpDir
 
-exit 0
+exit 0
\ No newline at end of file

detectors/normalize/bin/go_normalize.sh

@@ -27,12 +27,14 @@
 SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
 source ${SCRIPT_DIR}/../lib/lookforIR.lib.sh
 
+ORG_DEBUG=1
 
 pushTmpDir ORG.normalize
 
 	tmpfasta1="tmp_$$_1.fasta"
 	tmpfasta2="tmp_$$_2.fasta"
 
+	logdebug "Running on : $QUERY"
 
 	loginfo "Computing the genome size..."
 		genome_length=$(seqlength $QUERY)

detectors/normalize/lib/lookforIR.lib.sh

@@ -47,7 +47,9 @@ function lookForIR {
 }
 
 SCDB="${IR_DATA_DIR}/SC_RefDB"
-QUERY="${CALL_DIR}/$1"
 
-
-openLogFile "${QUERY/.*/}.log"
+if [[ ! "$1" =~ ^/ ]]; then
+	QUERY="${CALL_DIR}/$1"
+else
+	QUERY="$1"
+fi

detectors/normalize/tools/buildSCDB.sh

@@ -31,7 +31,7 @@ pushTmpDir ORG.buildSCDB
 	
 	
 	loginfo "Building LSC coorientation graph..."
-		${PROG_DIR}/coorienteSC.sh LSC.fasta 20000 ${LOGFILE} > LSC.tgf
+		${PROG_DIR}/coorienteSC.sh LSC.fasta 20000 ${ORG_LOGFILE} > LSC.tgf
 		${PROG_DIR}/cc.py LSC.tgf > LSC.cc
 		loginfo " --> $(awk '{print $1}' LSC.cc | uniq | wc -l) connected componants"
 	loginfo "Done"
@@ -73,7 +73,7 @@ pushTmpDir ORG.buildSCDB
 
 
 	loginfo "Checking LCS homogeneity..."
-		${PROG_DIR}/coorienteSC.sh LSC.direct.fasta 20000 ${LOGFILE} > LSC_RefDB.tgf		
+		${PROG_DIR}/coorienteSC.sh LSC.direct.fasta 20000 ${ORG_LOGFILE} > LSC_RefDB.tgf		
 		${PROG_DIR}/cc.py LSC_RefDB.tgf > LSC_RefDB.cc
 		NCC=$(awk '{print $1}' LSC_RefDB.cc | uniq | wc -l)
 		if (( $NCC == 1 )); then
@@ -103,7 +103,7 @@ pushTmpDir ORG.buildSCDB
 
 	
 	loginfo "Building SSC coorientation graph..."
-		${PROG_DIR}/coorienteSC.sh SSC.fasta 5000 ${LOGFILE} > SSC.tgf
+		${PROG_DIR}/coorienteSC.sh SSC.fasta 5000 ${ORG_LOGFILE} > SSC.tgf
 		${PROG_DIR}/cc.py SSC.tgf > SSC.cc
 		loginfo " --> $(awk '{print $1}' SSC.cc | uniq | wc -l) connected componants"
 	loginfo "Done"
@@ -146,7 +146,7 @@ pushTmpDir ORG.buildSCDB
 
 
 	loginfo "Checking SSC homogeneity..."
-		${PROG_DIR}/coorienteSC.sh SSC.direct.fasta 5000 ${LOGFILE} > SSC_RefDB.tgf		
+		${PROG_DIR}/coorienteSC.sh SSC.direct.fasta 5000 ${ORG_LOGFILE} > SSC_RefDB.tgf		
 		${PROG_DIR}/cc.py SSC_RefDB.tgf > SSC_RefDB.cc
 		NCC=$(awk '{print $1}' SSC_RefDB.cc | uniq | wc -l)
 		if (( $NCC == 1 )); then

detectors/trna/bin/go_trna.sh

+#!/bin/bash
+#
+#                           Annotate tRNA 
+#
+#========================================================================================
+#
+#  Annotate tRNA based on the Aragorn software predictions.
+
+#  go_trna.sh <FASTAFILE>
+#
+#		- <FASTAFILE> : The fasta file containing the genome to annotate
+#
+#  Results are printed to the standart output
+#
+#========================================================================================
+
+# -- 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"
+
+pushTmpDir ORG.trna
+
+	CAUTRNADB="${TRNA_DATA_DIR}/CAU_tRNA_DB.fasta"
+	export CAUTRNADB
+	
+	if [[ ! "$1" =~ ^/ ]]; then
+		QUERY="${CALL_DIR}/$1"
+	else
+		QUERY="$1"
+	fi
+
+	TRNA=$(basename ${QUERY})
+	
+	aragorn -i -w -seq ${QUERY} | \
+		${PROG_DIR}/../lib/aragorn_wrapper.awk
+	
+
+popTmpDir
+
+exit 0
+

detectors/trna/aragorn_wrapper.awk → detectors/trna/lib/aragorn_wrapper.awk

@@ -7,17 +7,9 @@ function genomeid() {
   return gid;
 }
 
-function home() {
-  "echo $ORGANNOT_HOME" | getline homedir;
-  return homedir;
-}
-
-function prog(program) {
-  return home() "/" program;
-}
-
-function trnalib(prognam) {
-  return home() "/lib/trnaCAU.ref.fasta";
+function trnalib() {
+  "echo $CAUTRNADB" | getline ref;
+  return ref
 }
 
 function awkPID() {
@@ -65,19 +57,20 @@ function patchtRNA(anticodon,trna,seq) {
   if (anticodon == "cat") {
     file=printfasta(trna "_" anticodon,seq,"");
 
-    command= prog("sumatra") " -d -n " file " " trnalib();
+    command= "sumatra -t 0.9 -x -n " file " " trnalib() " 2>> /dev/null";
     while ((command | getline output) > 0) {
       split(output,field," ");
-      n[field[2]]++;
-      d[field[2]]=field[3];
+      match(field[2],"trn.M?");
+      trna=substr(field[2],RSTART,RLENGTH);
+      n[trna]+=field[5];
     }
     close(command)
 
-    dmin=1;
+    nmax=0;
     for (i in n) {
-      dist=d[i]/n[i];
-      if (dist < dmin) {
-        dmin=dist;
+      dist=n[i];
+      if (n[i] > nmax) {
+        nmax=n[i];
         trna=i;
       }
     }
@@ -94,6 +87,42 @@ function gene2product(gene) {
   return "tRNA-" AA3[substr(gene,4,1)];
 }
 
+function emblTRNA(geneid,trna,loc,anti,intron,seq) {
+	if (loc ~ /^c/) {
+	     sub("c\\[","complement(",loc); 
+	     sub("\\]",")",loc);
+	     sub(",","..",loc)}
+	else {
+		sub("\\[","",loc);
+	    sub("\\]","",loc);
+	    sub(",","..",loc)}
+	    
+	anti=toupper(anti);
+    gsub("T","U",anti);
+    product=gene2product(trna);
+	
+	if (intron!="") {
+	   l=length(intron);
+       intron=substr(intron,2,l-2);
+       split(intron,intronpos,",");
+	   ib=intronpos[0];
+	   ie=intronpos[1];
+	   match(loc,"[0-9][0-9]*");
+	   gb=substr(loc,RSTART,RLENGTH);
+	   sub("\\.\\.",".." (gb + ib -2) "," (gb + ie) "..",loc); \
+	   sub("complement","complement(join",loc);\
+	   if (substr(loc,1,1) ~ /[0-9]/) {
+	      loc="join("loc} 
+	      loc=loc")"; 
+	      }
+	      
+	   print "FT   tRNA            " loc;
+	   print "FT                   /gene=\""trna"\"";
+	   print "FT                   /anticodon=\""anti"\"";	   
+	   print "FT                   /product=\""product"("anti")\"";
+	    
+}
+
 function gffTRNA(geneid,trna,loc,anti,intron,seq) {
   if (loc ~ /^c/) {
     complement="-";
@@ -139,7 +168,6 @@ function gffTRNA(geneid,trna,loc,anti,intron,seq) {
 }
 
 BEGIN {
-    print ARGV[1];
     AA1["Ala"]="A";
     AA1["Cys"]="C";
     AA1["Asp"]="D";
@@ -201,7 +229,7 @@ BEGIN {
      { seq=epissage(intron,seq);
        trna=patchtRNA(anti,trna,seq);
 #       print geneid,trna,loc,anti,"'"intron"'",seq;
-       gffTRNA(geneid,trna,loc,anti,intron,seq);
+       emblTRNA(geneid,trna,loc,anti,intron,seq);
        seq=""
      }
 
@@ -225,5 +253,5 @@ BEGIN {
 END  { seq=epissage(intron,seq);
        trna=patchtRNA(anti,trna,seq);
 #       print geneid,trna,loc,anti,"'"intron"'",seq;
-       gffTRNA(geneid,trna,loc,anti,intron,seq);
+       emblTRNA(geneid,trna,loc,anti,intron,seq);
      }

organnote.sh

+#!/bin/bash
+#
+#
+
+#
+#                           Annotate tRNA 
+#
+#========================================================================================
+#
+#  Annotate tRNA based on the Aragorn software predictions.
+
+#  go_trna.sh <FASTAFILE>
+#
+#		- <FASTAFILE> : The fasta file containing the genome to annotate
+#
+#  Results are printed to the standart output
+#
+#========================================================================================
+
+# -- 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"
+
+pushTmpDir ORG.organnot
+
+	if [[ ! "$1" =~ ^/ ]]; then
+		QUERY="${CALL_DIR}/$1"
+	else
+		QUERY="$1"
+	fi
+
+	RESULTS=$(basename ${QUERY/.*/})
+	LOG="${CALL_DIR}/${RESULTS}.log"
+	
+	rm -f ${LOG}
+	openLogFile ${LOG}
+
+	${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
+	
+	${PROG_DIR}/detectors/ir/bin/go_ir.sh ${QUERY} > "${RESULTS}.annot"		
+	${PROG_DIR}/detectors/trna/bin/go_trna.sh ${QUERY} >> "${RESULTS}.annot"
+	
+	cat "${RESULTS}.annot"
+	
+popTmpDir
+

scripts/bash_init.sh

@@ -19,11 +19,18 @@ function getAbsolutePath {
 function pushTmpDir {
 	TMP_DIR=$(mktemp -d -t "$1_proc_$$_")
 	pushd $TMP_DIR >& /dev/null
+	TMP_DIR_STACK="$TMP_DIR $TMP_DIR_STACK"
+	logdebug "Pushing temp directory $TMP_DIR"
+	logdebug "Stack : ${TMP_DIR_STACK}"
 }
 
 function popTmpDir {
+	TMP_DIR=$(echo $TMP_DIR_STACK | awk '{print $1}')
+	TMP_DIR_STACK=$(echo $TMP_DIR_STACK | awk '{$1="";print $0}')
 	popd  >& /dev/null
 	rm -rf $TMP_DIR >& /dev/null
+	logdebug "Poping temp directory $TMP_DIR"
+	logdebug "Stack : ${TMP_DIR_STACK}"
 }
 
 # Logging functions
@@ -34,32 +41,42 @@ function errcho {
 }
 
 function openLogFile {
-	LOGFILE=$1
-	touch ${LOGFILE}
+	ORG_LOGFILE=$1
+	export ORG_LOGFILE
+	touch ${ORG_LOGFILE}
 }
 
 
 function loginfo {
     errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO   ] $$ -- $1"
-    if [[ ! -z ${LOGFILE} ]]; then
-          echo `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO   ] $$ -- $1" >> ${LOGFILE}
+    if [[ ! -z ${ORG_LOGFILE} ]]; then
+          echo `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO   ] $$ -- $1" >> ${ORG_LOGFILE}
     fi
 }
 
 function logerror {
     errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR  ] $$ -- $1"
-    if [[ ! -z ${LOGFILE} ]]; then
-          echo `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR   ] $$ -- $1" >> ${LOGFILE}
+    if [[ ! -z ${ORG_LOGFILE} ]]; then
+          echo `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR   ] $$ -- $1" >> ${ORG_LOGFILE}
     fi
 }
 
 function logwarning {
     errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1"
-    if [[ ! -z ${LOGFILE} ]]; then
-          echo `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1" >> ${LOGFILE}
+    if [[ ! -z ${ORG_LOGFILE} ]]; then
+          echo `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1" >> ${ORG_LOGFILE}
     fi
 }
 
+function logdebug {
+	if [[ ! -z ${ORG_DEBUG} ]]; then
+	    errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA DEBUG  ] $$ -- $1"
+	    if [[ ! -z ${ORG_LOGFILE} ]]; then
+	          echo `date +'%Y-%m-%d %H:%M:%S'` "[OA DEBUG  ] $$ -- $1" >> ${ORG_LOGFILE}
+	    fi
+	fi
+}
+
 # Sequence related functions	
 	
 # Counts how many sequences are stored in a fasta file