A new set of protein cleaned for the CDS detector prepared using the

clusterizecore.sh script from the detectors/cds/lib folder.

The CDS detector is now modified to use the clean.fst files.


Former-commit-id: e30a53b5b6b658388af4b2640b30e6765c729894
Former-commit-id: 3015ad50d25248fb117ab00e816b00fde1f9ba1d

detectors/cds/bin/do_exonerate.csh

@@ -31,7 +31,7 @@ set GenoName = `basename $GenoFile:r`
 
 set ProtFile = $Argv[1]; Shift
 set ProtDir  = `dirname $ProtFile`
-set ProtName = `basename $ProtFile:r`
+set ProtName = `basename $ProtFile | $AwkCmd -F'.' '{print $1}'`
 set ProtType = `basename $ProtDir`
 
 NeedFile $GenoFile
@@ -122,7 +122,7 @@ endif
 
 if ($PASS1_SPEEDUP != 0) then
 
-  tcsh -f $PROG_DIR/do_filterbx.sh $GenoFile $ProtFile  \
+  tcsh -f $PROG_DIR/do_filterbx.csh $GenoFile $ProtFile  \
             $PASS1_BLASTX_FILTER_IDMIN          \
             $PASS1_BLASTX_FILTER_NBMIN          \
             $PASS1_BLASTX_FILTER_NBMAX > D_$$

detectors/cds/bin/go_cds.csh

@@ -55,10 +55,10 @@ endif
 
 foreach dir ("core" "shell" "dust")
   if (-d $DbRoot/$dir) then
-    set fams = `ls $DbRoot/$dir/*.fst`
+    set fams = `ls $DbRoot/$dir/*.clean.fst`
     Notify "running pass1:$dir exonerate of $Genome on $DbRoot"
     foreach f ($fams)
-      tcsh -f $PROG_DIR/do_exonerate.sh $Fasta $f $DbRoot/models $temp
+      tcsh -f $PROG_DIR/do_exonerate.csh $Fasta $f $DbRoot/models $temp
     end
   endif
 end

detectors/cds/lib/bestclust.awk

@@ -3,6 +3,8 @@
 #
 # -v MAX_SPAN ALLOW_STOP EXCLUDE
 #
+# 
+#
 
 BEGIN {
   PROCINFO["sorted_in"] = "@ind_num_asc"

detectors/cds/lib/clustertizecore.sh

@@ -6,6 +6,9 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh"
 
 CORELIB="${CDS_DATA_DIR}/chlorodb/core"
 
+CDHIT_ID=0.7
+CDHIT_DELTA=0.8
+
 
 function clusterize() {
  
@@ -17,12 +20,15 @@ function clusterize() {
  	rm -rf "${prot}"
  	mkdir -p "${prot}"
  	
- 	cd-hit -i "${fastain}" \
- 	       -o "${prot}/${cdhitout}" \
- 	       -c 0.6 -G 1 \
- 	       -g 1 -s 0.8 \
- 	       -b 150 -p 1 \
- 	       -d 0 -n 3
+ 	cd-hit 	-i "${fastain}" \
+ 	    	-o "${prot}/${cdhitout}" \
+ 	    	-c ${CDHIT_DELTA} \
+ 	    	-G 1 \
+			-g 1 \
+			-aL 0.95 \
+			-s ${CDHIT_ID} \
+ 	    	-b 350 -p 1 \
+ 	    	-d 0 -n 3
  	       
  	fasta1line "${fastain}" > "${prot}/${fasta1}"
  	
@@ -35,6 +41,8 @@ function clusterize() {
  	                 filename=prot".cluster."cluster".ids"; \
  	                 print $3 >> filename ; \
  	                 close(filename) }' "${cdhitout}.clstr"
+ 	                
+ 	rm -f "../$prot.clean.fst"
  	                 
  	for ids in *.cluster.*.ids ; do
  		cluster=$(printf "%03d" $(echo "${ids}" | $AwkCmd -F'.' '{print $3}'))
@@ -52,10 +60,10 @@ function clusterize() {
 	 	    egrep -v -- '^--$' > "$alignment"
 	    fi
 	 		
- 	    if (( size >= 10 )) ; then
+ 	    if (( size >= 5 )) ; then
  	    	egrep -f "$ids" -A 1 "${fasta1}" | \
 	 	    egrep -v -- '^--$' | \
-	 	    formatfasta >> "$prot.clean.fst"
+	 	    formatfasta >> "../$prot.clean.fst"
  	    fi
  	    
  	    rm -f "$ids"
@@ -73,6 +81,8 @@ function clusterize() {
 
 pushd $CORELIB
 
+rm -rf *.clean.fst
+
 for prot in *.fst ; do
 	prot="${prot/.fst/}"
 	clusterize "$prot"