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/go_cds.sh

@@ -1,89 +0,0 @@
-#!/usr/bin/env tcsh -f
-#
-#                           Annotate CDS 
-#
-#========================================================================================
-#
-#  Annotate CDS
-#
-#  go_cds.sh <FASTAFILE>
-#
-#		- <FASTAFILE> : The fasta file containing the genome to annotate
-#
-#  Results are printed to the standard output
-#
-#========================================================================================
-# usage: go_cds.sh fasta [db_root]
-#
-unsetenv ORG_SOURCED
-
-setenv ORG_HOME `dirname $0`/../../..
-source $ORG_HOME/scripts/csh_init.sh
-
-NeedArg 1
-
-set Fasta = $Argv[1]; Shift
-
-NeedFile $Fasta
-
-set Genome = `basename $Fasta:r`
-
-set DbRoot = $CDS_DATA_DIR/chlorodb
-
-if ($#Argv > 0) then
-  set DbRoot = $Argv[1]; Shift
-endif
-
-NeedDir $DbRoot/core
-NeedFile $DbRoot/core/Annot.lst
-
-NeedDir $DbRoot/models
-
-#
-# run everything into temporary place
-#
-
-set temp = $Genome.tmp
-if (! -d $temp) then
-  Notify "making directory $temp"
-  mkdir $temp
-endif
-
-#
-# pass1: run exonerate
-#
-
-foreach dir ("core" "shell" "dust")
-  if (-d $DbRoot/$dir) then
-    set fams = `ls $DbRoot/$dir/*.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
-    end
-  endif
-end
-
-#
-# pass2: transsplicing
-#
-
-#
-# pass3: prokov
-#
-
-#
-# end : output on stdout
-#
-
-cat $temp/*.res
-
-# cleanup everything
-
-AssignUndef TMP_CLEANUP 1
-
-if ($TMP_CLEANUP != 0) then
-  Notify "  cleanup $temp"
-  (\rm -r $temp) >& /dev/null
-endif
-
-Exit 0