Adds detection of RPS12 and managment of locus tags

Former-commit-id: b9b17708eaaa27580f1e99bd3c375d4b6aba4d79
Former-commit-id: 369361ffa58e65b19ab1005bdf7960924f24ca08

detectors/cds/tools/go_rps12db.sh

@@ -0,0 +1,106 @@
+#!/bin/bash
+#
+#                           BUILD REFERENCE : THE RPS12 LIBRARY
+#
+#========================================================================================
+
+# -- 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"
+source "${THIS_DIR}/lib/clusterize_prot.sh"
+
+function extract_rps12() {
+$AwkCmd '                                          \
+      /^LOCUS/    {LOCUS=$2;}                      \
+      /^     [^ ]/ { if (CDS) {                    \
+                        print LOCUS "/" feature;   \
+                        print "#################"  \
+                       }                           \
+                    CDS=0;                         \
+                   }                               \
+      /^     CDS / {CDS=1;                         \
+                    $1="";                         \
+                    feature=""}                    \
+      (CDS)        { sub(/^ */,"",$0);             \
+                     sub(/ *$/,"",$0);             \
+                     feature=feature $0}           \
+    ' \
+    | egrep -i '"rps12"'  \
+    | $AwkCmd -F"/" '                              \
+       function printfasta(seq) {                  \
+             seqlen=length(seq);                   \
+             for (i=1; i <= seqlen; i+=60)         \
+                 print substr(seq,i,60);           \
+             }                                     \
+                                                   \
+                ($1 != current) {current=$1;       \
+                                  n=1              \
+                                 }                 \
+                 {$1=$1 "_rps12_" n;               \
+                  n++;                             \
+                  delete keys;                     \
+                  for (i=3; i<=NF; i++) {          \
+                      split($i,key,"=");           \
+                      keys[key[1]]=key[2]          \
+                  }                                \
+                  prot = keys["translation"];      \
+                  gsub(/"/,"",prot);               \
+                  print ">" $1,"location=" $2 ";"; \
+                  printfasta(prot)                 \
+                 }                                 \
+    ' 
+}
+
+
+pushTmpDir ORG.buildRPS12DB
+
+	RPS12FILE=RPS12_prot.fst	
+
+	openLogFile "${CDS_DATA_DIR}/chlorodb/RPS12_DB.log"
+
+	loginfo "Selecting Viridiplantae genbank entries..."
+		VIRIDIPLANTAE=$(${PROG_DIR}/../../normalize/tools/selectViridiplantae.sh $*) 
+		loginfo " --> $(echo ${VIRIDIPLANTAE} | wc -w) entries selected"
+	loginfo "Done"
+
+    loginfo "Extracting the RPS12 protein sequences from the plants entries..."
+        ( for gbk in ${VIRIDIPLANTAE} ; do
+            gzcat $gbk | \
+                extract_rps12 
+          done ) > ${RPS12FILE}
+	loginfo "Done"
+
+	loginfo "Installing the RPS12 protein sequence database..."
+		
+		cp ${RPS12FILE} "${CDS_DATA_DIR}/chlorodb/RPS12_DB.fst"
+
+	loginfo "Done"
+
+popTmpDir
+
+pushd "${CDS_DATA_DIR}/chlorodb"
+
+	loginfo "Clusterizing the RPS12 protein sequence database..."
+    rm -rf RPS12_DB.clean.fst
+    clusterize RPS12_DB
+	loginfo "Done"
+
+    loginfo "  formatting Blast RPS12 DB"
+    timeoutcmd 300 makeblastdb -dbtype prot -in RPS12_DB.clean.fst >& /dev/null
+	loginfo "Done"
+
+
+
+popd
+
+#
+# format blast protein database
+#
+
+
+
+
+loginfo "Done"
+

detectors/rrna/bin/go_rrna.sh

@@ -49,6 +49,7 @@ pushTmpDir ORG.rrna
 		                print "FT   rRNA            " loc; \
 		                  print "FT                   /gene=\""rrna" rRNA\""
 		                  print "FT                   /product=\""rrna" ribosomal RNA\""
+						  print "FT                   /locus_tag=\"\"";
 		                full=0
 		                }'	
 

detectors/trna/lib/aragorn_wrapper.awk

@@ -167,7 +167,9 @@ function emblTRNA(geneid,trna,loc,anti,intron,notes,seq) {
 	   print "FT   tRNA            " loc;
 	   print "FT                   /gene=\""trna"\"";
 	   print "FT                   /anticodon=\""anti"\"";	   
+#	   print "FT                   /note=\"*anticodon: "anti"\"";
 	   print "FT                   /product=\""product"("anti")\"";
+     print "FT                   /locus_tag=\"\"";
 #	   print "FT                   /inference=\"Aragorn-1.2.38\"";
 	   if (notes!="-")
 		   print "FT                   /note=\""notes"\"";