Patch RPS12 detection

detectors/cds/bin/do_rps12.sh

@@ -31,6 +31,10 @@ else
 	QUERY="$1"
 fi
 
+shift
+
+GENOME_LENGHT="$2"
+
 if (( $# > 1 )) ; then
     TEMP=$2
 else
@@ -45,7 +49,6 @@ AnnotFile="$CDS_DATA_DIR/sp_chlorodb/Annot.lst"
 ModelsDir="$CDS_DATA_DIR/sp_chlorodb/models"
 
 SEQLEN=$(seqlength "${QUERY}")
-SEQUENCE=$(readfirstfastaseq "${QUERY}") 
 
 pushTmpDir ORG.RPS12
 
@@ -78,7 +81,10 @@ blastx \
                 {PREV_CDS = $2;}
                 
                 (BEST_EVAL > ($11 + 0.0)) {BEST_EVAL = ($11 + 0.0)} 
-          ' > "rps12_locate.hsps"
+          ' \
+    | $AwkCmd -v glength=${GENOME_LENGHT}  \
+              '!($7 + 0 > glength +  0 && $8  + 0 > glength +  0)' \
+    > "rps12_locate.hsps"
 
     
     #

detectors/cds/bin/go_cds.sh

@@ -9,6 +9,7 @@
 #  go_cds.sh <FASTAFILE> [DBROOT]
 #
 #		- <FASTAFILE> : The fasta file containing the genome to annotate
+#   - <GENOME_LENGHT> : The length of the genome to annotate
 #       - [DBROOT]    : optionnal argument allowing to specify database directory
 #
 #  Results are printed to the standard output
@@ -28,12 +29,14 @@ else
   Threads=$ANNOT_MAXCPU
 fi
 
-needarg 1
+needarg 2
 
 Fasta=$1; shift
 
 needfile "$Fasta"
 
+GenomeLength=$1; shift
+
 # Genome names is set from the base
 # name of the genome file without its extension
 Genome=$(basename ${Fasta%.*})
@@ -92,7 +95,7 @@ fi
 
 if [[ "$cdsdetection_pass2" == "yes" ]] ; then
     loginfo "running pass2:rps12 exonerate of $Genome on $DbRoot"
-    $PROG_DIR/do_rps12.sh $Fasta $temp
+    $PROG_DIR/do_rps12.sh $Fasta $GenomeLength $temp
 fi
 
 #

detectors/cds/lib/rps12_filter_4.awk

@@ -34,6 +34,7 @@ function convert(p1,p2) {
     r = $0
     while (length(s) > 0) {
         match(s,/[0-9]+\.\.[0-9]+/)
+        if (RLENGTH+0 < 0) break
         range = substr(s,RSTART,RLENGTH)
         s = substr(s,RSTART+RLENGTH+1)
         match(range,/^[0-9]+/)

org-annotate.sh

@@ -441,6 +441,7 @@ do
     shift
 done
 
+
 loginfo "Locus tag prefix provided: $tagprefix"
 loginfo "Locus tag numbered from..: $locusshift"
 loginfo "NCBI taxid provided......: $taxid"
@@ -572,7 +573,7 @@ pushTmpDir ORG.organnot
 							    cdsdetection_pass1=$cdsdetection_pass1 \
 								cdsdetection_pass2=$cdsdetection_pass2 \
 								cdsdetection_pass3=$cdsdetection_pass3 \
-								${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
+								${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" "$sl" >> "${RESULTS}.annot"
 							loginfo "Done."
 						fi