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