Switch to a swissprot based reference database for CDS annotation

Former-commit-id: 3da31ce8a135394ecac041291134d61f11f06d8f
Former-commit-id: 406f41a7cb2db14ea832480b86f72a11d3b0ab4a

detectors/cds/bin/do_exonerate.csh

@@ -6,10 +6,13 @@
 #
 #  Annotate CDS using exonerate
 #
-#  do_exonerate.sh <FASTAGENOM> <FASTAPROT> [<OUTDIR>]
+#  do_exonerate.sh <PASS> <FASTAGENOM> <FASTAPROT> <ANNOTFILE> <MODELDIR> [<OUTDIR>]
 #
+#   - <PASS>       : the pass running exonarate
 #		- <FASTAGENOM> : The fasta file containing the genome to annotate
 #		- <FASTAPROT>  : The fasta file containing the protein family
+#   - <ANNOTFILE>  : The annotation file used to add product info
+#	  - <MODELDIR>   : Directory containing model parameters for exonerate
 #
 #  Results are in file : `basename <FASTAGENOM>:r`.`basename <FASTAPROT>:r`.res 
 #
@@ -26,17 +29,21 @@ alias Override 'if (-e \!:2) set \!:1 = \!:2'
 
 NeedArg 2
 
+set Pass = $Argv[1]; Shift
 set GenoFile = $Argv[1]; Shift
 set GenoName = `basename $GenoFile:r`
 
 set ProtFile = $Argv[1]; Shift
 set ProtDir  = `dirname $ProtFile`
+set DBDir    = `dirname $ProtDir`
 set ProtName = `basename $ProtFile | $AwkCmd -F'.' '{print $1}'`
 set ProtType = `basename $ProtDir`
 
+set AnnotFile = $Argv[1]; Shift
+
 NeedFile $GenoFile
 NeedFile $ProtFile
-NeedFile $ProtDir/Annot.lst
+NeedFile $AnnotFile
 
 set ModelsDir = $PROG_DIR/../models
 if ($#Argv > 0) then
@@ -188,7 +195,7 @@ if ( -z $base.exo.best) then
 		$AwkCmd -v MAX_SPAN=$PASS1_MAX_SPAN         \
 		        -v ALLOW_STOP=1     \
 		        -v EXCLUDE=$GenoName                \
-		        -f $LIB_DIR/bestclust.awk $base.exo.raw > $base.exo.best		
+		        -f $LIB_DIR/bestclust.awk $base.exo.raw > $base.exo.best	
 	endif
 endif
 
@@ -196,7 +203,16 @@ endif
 # get annotations
 #
 
-egrep "^$ProtName " $ProtDir/Annot.lst | $AwkCmd '{print "c annot", $0}' > T_$$
+set sp_match=`awk '/^e similarity/ {print $12}' $base.exo.best | head -1`
+
+if ( ${%sp_match} > 0 ) then
+  set sp_ac=`awk -v sp="$sp_match" '($1 ~ sp) {sub(/SP_AC=/,"",$2); sub(/;$/,"",$2); print $2} ' $DbFile`
+   echo "             " patch ac $sp_match to $sp_ac > /dev/stderr
+  sed "s/$sp_match/$sp_ac/g" $base.exo.best > T_$$
+  mv T_$$ $base.exo.best
+endif
+
+egrep "^$ProtName " $AnnotFile | $AwkCmd '{print "c annot", $0}' > T_$$
 
 #
 # extend start/stop
@@ -213,7 +229,7 @@ $AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk             \
 # translate
 #
 
-echo "c pass pass1 $ProtType" > $base.iff
+echo "c pass $Pass $ProtType" > $base.iff
 
 $AwkCmd -v FASTA=$GenoFile -f $LIB_DIR/libutil.awk \
         -f $LIB_DIR/translate.awk T_$$ >> $base.iff

detectors/cds/bin/do_rps12.sh

@@ -37,10 +37,13 @@ else
     TEMP=""
 fi
 
-DBROOT="$CDS_DATA_DIR/chlorodb/RPS12"
-RPS12DB="${DBROOT}/RPS12_DB.clean.fst"
+DBROOT="$CDS_DATA_DIR/sp_chlorodb/RPS12"
+RPS12DB="${DBROOT}/rps12.fst"
 DELTA=50
 
+AnnotFile="$CDS_DATA_DIR/sp_chlorodb/Annot.lst"
+ModelsDir="$CDS_DATA_DIR/sp_chlorodb/models"
+
 SEQLEN=$(seqlength "${QUERY}")
 SEQUENCE=$(readfirstfastaseq "${QUERY}") 
 
@@ -61,7 +64,9 @@ blastx \
                 BEGIN {BEST_EVAL = 1e-40; 
                        OUT = 0} 
                 /^#/ {next} 
-                ($2 == PREV_CDS) { HSPs = HSPs "\n" $0;} 
+                ($2 == PREV_CDS) && (($11 + 0.0) < (1e-5 + 0.0)) { 
+                    HSPs = HSPs "\n" $0;
+                    } 
                 
                 (OUT < 20) && ($2 != PREV_CDS) && (BEST_EVAL < (1e-20 + 0.0)) { 
                     if (PREV_CDS) print HSPs; 
@@ -75,6 +80,7 @@ blastx \
                 (BEST_EVAL > ($11 + 0.0)) {BEST_EVAL = ($11 + 0.0)} 
           ' > "rps12_locate.hsps"
 
+    
     #
     # Extracting protein ids from selected blast HSPs
     #
@@ -83,7 +89,6 @@ blastx \
         | sort \
         | uniq > "dbsel.txt"
 
-
     #
     # Extract corresponding protein sequences
     # from the RPS12 database.
@@ -134,7 +139,7 @@ blastx \
                         }
                     }
         ' \
-        | sort -nk 3 \
+        | sort -nk 3  \
         | $AwkCmd '($3 != old3 || $4 != old4) { 
                           i++
                           old3=$3 
@@ -262,13 +267,14 @@ blastx \
     # It should be one or two fragments
     #
         export PASS1_SPEEDUP=0
-        cp $DBROOT/Annot.lst RPS12
-        nbseq = 0
+        nbseq=0
         for fasta in rps12_fragments_*.fasta ; do
             tcsh -f ${PROG_DIR}/do_exonerate.csh \
+                Pass2 \
                 $fasta \
                 "RPS12/rps12.fasta" \
-                $DBROOT/../models $(pwd)
+                $AnnotFile \
+                $ModelsDir $(pwd)
             ((nbseq=nbseq+1))
         done
 

detectors/cds/bin/go_cds.sh

@@ -35,19 +35,22 @@ Genome=$(basename ${Fasta%.*})
 # DbRoot is set to its default values except 
 # if the second argument precise another DbRoot
 
-DbRoot="$CDS_DATA_DIR/chlorodb"
+DbRoot="$CDS_DATA_DIR/sp_chlorodb"
 
 if (( $# > 0)) ; then
   DbRoot="$1"; Shift
 fi
 
+AnnotFile="$DbRoot/Annot.lst" 
+
 needdir $DbRoot
 needdir $DbRoot/core
-needfile $DbRoot/core/Annot.lst
+needfile $AnnotFile
 needdir $DbRoot/models
 
 assignundef cdsdetection_pass1 yes
 assignundef cdsdetection_pass2 yes
+assignundef cdsdetection_pass3 yes
 
 temp=$(mktempdir $(hostname))
 
@@ -63,33 +66,47 @@ Fasta="$temp/genome.fasta"
 #
 
 if [[ "$cdsdetection_pass1" == "yes" ]] ; then
-    for dir in "core" "shell" "dust" ; do
+    for dir in "core" ; do
     if [[ -d $DbRoot/$dir ]] ; then
-        fams=$(ls $DbRoot/$dir/*.clean.fst)
+        fams=$(ls $DbRoot/$dir/*.fst)
         loginfo "running pass1:$dir exonerate of $Genome on $DbRoot"
         for f in $fams ; do
-        tcsh -f $PROG_DIR/do_exonerate.csh $Fasta $f $DbRoot/models $temp
+        tcsh -f $PROG_DIR/do_exonerate.csh Pass1 $Fasta $f $AnnotFile $DbRoot/models $temp
         done
     fi
     done
 
-    cp $temp/genome.cds.fasta $Genome.cds.fasta 
-
+    mv $temp/genome.cds.fasta $Genome.cds_pass1.fasta 
 fi
 
 
 #
-# pass2: transsplicing
+# pass2: RPS12 gene with transsplicing 
 #
 
 if [[ "$cdsdetection_pass2" == "yes" ]] ; then
+    loginfo "running pass2:rps12 exonerate of $Genome on $DbRoot"
     $PROG_DIR/do_rps12.sh $Fasta $temp
 fi
 
 #
-# pass3: prokov
+# pass3: run exonerate on shell and dust
 #
 
+if [[ "$cdsdetection_pass3" == "yes" ]] ; then
+    for dir in "shell" ; do
+    if [[ -d $DbRoot/$dir ]] ; then
+        fams=$(ls $DbRoot/$dir/*.fst)
+        loginfo $fams
+        loginfo "running pass3:$dir exonerate of $Genome on $DbRoot"
+        for f in $fams ; do
+          tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp
+        done
+    fi
+    done
+    mv $temp/genome.cds.fasta $Genome.cds_pass2.fasta 
+fi
+
 # $PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
 
 #