From 405631f527e6420c6523dfeb516a436513af2a03 Mon Sep 17 00:00:00 2001
From: alain viari <alain.viari@inria.fr>
Date: Fri, 13 Nov 2015 22:37:22 +0100
Subject: [PATCH] cds go_test bug fixed

Former-commit-id: f73133dca83d02a0c223e98a3ac82fdb0d03c5ae
Former-commit-id: 3db7c0037f7c109f4479490480d4323a55206c6a
---
 detectors/cds/bin/do_exonerate.sh             | 59 +++++++++++++------
 detectors/cds/bin/go_cds.sh                   | 26 ++++----
 detectors/cds/lib/toEmbl.awk                  | 14 +++++
 detectors/cds/params/default                  | 10 ++--
 detectors/cds/test/go_test.sh                 |  4 +-
 .../cds/test/test.db/{ => core}/Annot.lst     |  0
 .../cds/test/test.db/{ => core}/atpf.fst      |  0
 .../cds/test/test.db/{ => core}/ccsa.fst      |  0
 .../cds/test/test.db/{ => core}/ndha.fst      |  0
 .../cds/test/test.db/{ => core}/ndhb.fst      |  0
 .../cds/test/test.db/{ => core}/ndhd.fst      |  0
 .../cds/test/test.db/{ => core}/ndhe.fst      |  0
 .../cds/test/test.db/{ => core}/ndhf.fst      |  0
 .../cds/test/test.db/{ => core}/ndhg.fst      |  0
 .../cds/test/test.db/{ => core}/ndhh.fst      |  0
 .../cds/test/test.db/{ => core}/ndhi.fst      |  0
 .../cds/test/test.db/{ => core}/psac.fst      |  0
 .../cds/test/test.db/{ => core}/rpl2.fst      |  0
 .../cds/test/test.db/{ => core}/rpl23.fst     |  0
 .../cds/test/test.db/{ => core}/rpl32.fst     |  0
 .../cds/test/test.db/{ => core}/rps15.fst     |  0
 .../cds/test/test.db/{ => core}/rps7.fst      |  0
 .../cds/test/test.db/{ => core}/ycf1.fst      |  0
 .../cds/test/test.db/{ => core}/ycf2.fst      |  0
 .../cds/test/test.db/models/blosum62.mat      | 29 +++++++++
 .../cds/test/test.db/models/splice.none.frq   |  6 ++
 .../test/test.db/models/splice3.default.frq   | 13 ++++
 .../cds/test/test.db/models/splice3.ndha.frq  | 13 ++++
 .../cds/test/test.db/models/splice3.psba.frq  | 13 ++++
 .../test/test.db/models/splice5.default.frq   | 13 ++++
 .../cds/test/test.db/models/splice5.ndha.frq  | 13 ++++
 .../cds/test/test.db/models/splice5.psba.frq  | 13 ++++
 .../cds/test/test.db/models/start.default.frq |  8 +++
 .../cds/test/test.db/models/start.ndhd.frq    |  7 +++
 .../cds/test/test.db/models/start.rps19.frq   |  3 +
 .../cds/test/test.db/models/stop.default.frq  |  4 ++
 detectors/cds/test/test.ref                   | 18 ++++++
 scripts/csh_init.sh                           |  2 +-
 38 files changed, 231 insertions(+), 37 deletions(-)
 rename detectors/cds/test/test.db/{ => core}/Annot.lst (100%)
 rename detectors/cds/test/test.db/{ => core}/atpf.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ccsa.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ndha.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ndhb.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ndhd.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ndhe.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ndhf.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ndhg.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ndhh.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ndhi.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/psac.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/rpl2.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/rpl23.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/rpl32.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/rps15.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/rps7.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ycf1.fst (100%)
 rename detectors/cds/test/test.db/{ => core}/ycf2.fst (100%)
 create mode 100644 detectors/cds/test/test.db/models/blosum62.mat
 create mode 100644 detectors/cds/test/test.db/models/splice.none.frq
 create mode 100644 detectors/cds/test/test.db/models/splice3.default.frq
 create mode 100644 detectors/cds/test/test.db/models/splice3.ndha.frq
 create mode 100644 detectors/cds/test/test.db/models/splice3.psba.frq
 create mode 100644 detectors/cds/test/test.db/models/splice5.default.frq
 create mode 100644 detectors/cds/test/test.db/models/splice5.ndha.frq
 create mode 100644 detectors/cds/test/test.db/models/splice5.psba.frq
 create mode 100644 detectors/cds/test/test.db/models/start.default.frq
 create mode 100644 detectors/cds/test/test.db/models/start.ndhd.frq
 create mode 100644 detectors/cds/test/test.db/models/start.rps19.frq
 create mode 100644 detectors/cds/test/test.db/models/stop.default.frq

diff --git a/detectors/cds/bin/do_exonerate.sh b/detectors/cds/bin/do_exonerate.sh
index 5fbe664..4985767 100755
--- a/detectors/cds/bin/do_exonerate.sh
+++ b/detectors/cds/bin/do_exonerate.sh
@@ -15,47 +15,66 @@
 #
 #========================================================================================
 #
-# usage: do_exonerate.sh dna.fasta prot.fasta [outdir]
+# usage: do_exonerate.sh dna.fasta prot.fasta [model_dir [out_dir]]
 #
 unsetenv ORG_SOURCED
 
 setenv ORG_HOME `dirname $0`/../../..
 source $ORG_HOME/scripts/csh_init.sh
 
-set PARAMS_DIR = $LIB_DIR/../params
-set MODELS_DIR = $LIB_DIR/../models
-
 alias Override 'if (-e \!:2) set \!:1 = \!:2'
 
 NeedArg 2
 
-set GenoFile = $Argv[1]
+set GenoFile = $Argv[1]; Shift
 set GenoName = `basename $GenoFile:r`
 
-set ProtFile = $Argv[2]
+set ProtFile = $Argv[1]; Shift
 set ProtDir  = `dirname $ProtFile`
 set ProtName = `basename $ProtFile:r`
+set ProtType = `basename $ProtDir`
 
 NeedFile $GenoFile
 NeedFile $ProtFile
 NeedFile $ProtDir/Annot.lst
 
+set ModelsDir = $PROG_DIR/../models
+if ($#Argv > 0) then
+  set ModelsDir = $Argv[1]; Shift
+  Notify "  exonerate models : $ModelsDir"
+else
+  Warning "  using default exonerate models : $ModelsDir"
+endif
+
+NeedFile $ModelsDir/start.default.frq
+NeedFile $ModelsDir/stop.default.frq
+NeedFile $ModelsDir/splice3.default.frq
+NeedFile $ModelsDir/splice5.default.frq
+
 set OutDir = .
-if ($#Argv >= 3) set OutDir = $3
+if ($#Argv > 0) then 
+  set OutDir = $Argv[1]; Shift
+endif
+
 if (! -d $OutDir) mkdir $OutDir
 
+set ParamsDir = $PROG_DIR/../params
+
+NeedFile $ParamsDir/default
+
 #
 # general parameters
 #
 
-source $PARAMS_DIR/default
+source $ParamsDir/default
 
 #
 # family specific parameters
 #
 
-if (-e $PARAMS_DIR/$ProtName) then
-  source $PARAMS_DIR/$ProtName
+if (-e $ParamsDir/$ProtName) then
+  Notify "  override parameters with $ParamsDir/$ProtName"
+  source $ParamsDir/$ProtName
 endif
 
 #
@@ -63,23 +82,23 @@ endif
 #
 
 if ($?STARTMODEL == 0) then
-  set STARTMODEL = $MODELS_DIR/start.default.frq
-  Override STARTMODEL $MODELS_DIR/start.$ProtName.frq
+  set STARTMODEL = $ModelsDir/start.default.frq
+  Override STARTMODEL $ModelsDir/start.$ProtName.frq
 endif
 
 if ($?STOPMODEL == 0) then
-  set STOPMODEL = $MODELS_DIR/stop.default.frq
-  Override STOPMODEL $MODELS_DIR/stop.$ProtName.frq
+  set STOPMODEL = $ModelsDir/stop.default.frq
+  Override STOPMODEL $ModelsDir/stop.$ProtName.frq
 endif
 
 if ($?SPLICE3MODEL == 0) then
-  set SPLICE3MODEL = $MODELS_DIR/splice3.default.frq
-  Override SPLICE3MODEL $MODELS_DIR/splice3.$ProtName.frq
+  set SPLICE3MODEL = $ModelsDir/splice3.default.frq
+  Override SPLICE3MODEL $ModelsDir/splice3.$ProtName.frq
 endif
 
 if ($?SPLICE5MODEL == 0) then
-  set SPLICE5MODEL = $MODELS_DIR/splice5.default.frq
-  Override SPLICE5MODEL $MODELS_DIR/splice5.$ProtName.frq
+  set SPLICE5MODEL = $ModelsDir/splice5.default.frq
+  Override SPLICE5MODEL $ModelsDir/splice5.$ProtName.frq
 endif
 
 #
@@ -178,8 +197,10 @@ $AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk             \
 # translate
 #
 
+echo "c pass pass1 $ProtType" > $base.iff
+
 $AwkCmd -v FASTA=$GenoFile -f $LIB_DIR/libutil.awk \
-        -f $LIB_DIR/translate.awk T_$$ > $base.iff
+        -f $LIB_DIR/translate.awk T_$$ >> $base.iff
 
 #
 # convert to embl
diff --git a/detectors/cds/bin/go_cds.sh b/detectors/cds/bin/go_cds.sh
index f38e053..487d458 100755
--- a/detectors/cds/bin/go_cds.sh
+++ b/detectors/cds/bin/go_cds.sh
@@ -13,7 +13,7 @@
 #  Results are printed to the standard output
 #
 #========================================================================================
-# usage: go_cds.sh fasta [db_core]
+# usage: go_cds.sh fasta [db_root]
 #
 unsetenv ORG_SOURCED
 
@@ -28,13 +28,16 @@ NeedFile $Fasta
 
 set Genome = `basename $Fasta:r`
 
-set DbCore = $CDS_DATA_DIR/chlorodb/core
+set DbRoot = $CDS_DATA_DIR/chlorodb
 
 if ($#Argv > 0) then
-  set DbCore = $Argv[1]; Shift
+  set DbRoot = $Argv[1]; Shift
 endif
 
-NeedFile $DbCore/Annot.lst
+NeedDir $DbRoot/core
+NeedFile $DbRoot/core/Annot.lst
+
+NeedDir $DbRoot/models
 
 #
 # run everything into temporary place
@@ -50,15 +53,16 @@ endif
 # pass1: run exonerate
 #
 
-set fams = `ls $DbCore/*.fst`
-
-Notify "running pass1: exonerate of $Genome on $DbCore"
-
-foreach f ($fams)
-  $PROG_DIR/do_exonerate.sh $Fasta $f $temp
+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)
+      $PROG_DIR/do_exonerate.sh $Fasta $f $DbRoot/models $temp
+    end
+  endif
 end
 
-
 #
 # pass2: transsplicing
 #
diff --git a/detectors/cds/lib/toEmbl.awk b/detectors/cds/lib/toEmbl.awk
index e6df42d..1ebfa7c 100644
--- a/detectors/cds/lib/toEmbl.awk
+++ b/detectors/cds/lib/toEmbl.awk
@@ -67,10 +67,20 @@ function QQualifier(qual, val) {
   SQualifier(qual, "\"" val "\"")
 }
 
+function Unk(s) {
+  return (s =="" ? "none" : s)
+}
+
 #
 # rules
 #
 
+/^c pass/ {
+  PassType = $3
+  PassInfo = $NF
+  next
+}
+
 /^c annot/ {
   GeneName = $4
   Product = $NF
@@ -113,6 +123,9 @@ function QQualifier(qual, val) {
 
 /^c end_entry/ {
 
+  GeneName = Unk(GeneName)
+  PassType = Unk(PassType)
+  
   gname = (Ngene == 1 ? GeneName : GeneName "_" ++Igene)
   locus = ""
   
@@ -127,6 +140,7 @@ function QQualifier(qual, val) {
   QQualifier("locus_tag", locus)
   QQualifier("product", Product)
   QQualifier("inference", "similar to DNA sequence:" Simil)
+  QQualifier("inference", "detect pass:" PassType ":" PassInfo)
   QQualifier("translation", Translat)
   
   if (Nexon > 1) {
diff --git a/detectors/cds/params/default b/detectors/cds/params/default
index 1797145..0e7ac2f 100644
--- a/detectors/cds/params/default
+++ b/detectors/cds/params/default
@@ -2,9 +2,11 @@
 # CDS Searching parameters
 #
 
+Notify "  using default exonerate parameters"
+
 #
 # general parameters 
-# (may be overriden by enviroment variables)
+# may be overriden by enviroment variables (AssignUndef)
 #
 
 AssignUndef TMP_CLEANUP 1
@@ -30,11 +32,11 @@ AssignUndef PASS1_BESTN         10
 AssignUndef PASS1_FRAMESHIFT    -100
 
 # pass1: exonerate use Blosum62 with larger penalty for Stops
-AssignUndef PASS1_SUBMAT $MODELS_DIR/blosum62.mat
+AssignUndef PASS1_SUBMAT $ModelsDir/blosum62.mat
 
 # comment next lines to use default or specific splice model
-# AssignUndef SPLICE3MODEL $MODELS_DIR/splice.none.frq
-# AssignUndef SPLICE5MODEL $MODELS_DIR/splice.none.frq
+# AssignUndef SPLICE3MODEL $ModelsDir/splice.none.frq
+# AssignUndef SPLICE5MODEL $ModelsDir/splice.none.frq
 
 #
 # pass1: cluster selection parameters
diff --git a/detectors/cds/test/go_test.sh b/detectors/cds/test/go_test.sh
index 9e62ae4..fad2596 100755
--- a/detectors/cds/test/go_test.sh
+++ b/detectors/cds/test/go_test.sh
@@ -1,6 +1,6 @@
 #!/bin/csh -f
 
-setenv Verbose 1
+setenv Verbose 0
 
 setenv ORG_HOME `dirname $0`/../../..
 source $ORG_HOME/scripts/csh_init.sh
@@ -20,7 +20,7 @@ set stat = $status
 
 if ($stat == 0) then
   echo "+ $VTC[3]CDS test Ok$VTC[1]"
-  \rm -r test.bak test.tmp test.db/*.fst.p??
+  \rm -r test.bak test.tmp test.db/core/*.fst.p??
 else
   echo "* $VTC[2]CDS test Failure$VTC[1]"
 endif
diff --git a/detectors/cds/test/test.db/Annot.lst b/detectors/cds/test/test.db/core/Annot.lst
similarity index 100%
rename from detectors/cds/test/test.db/Annot.lst
rename to detectors/cds/test/test.db/core/Annot.lst
diff --git a/detectors/cds/test/test.db/atpf.fst b/detectors/cds/test/test.db/core/atpf.fst
similarity index 100%
rename from detectors/cds/test/test.db/atpf.fst
rename to detectors/cds/test/test.db/core/atpf.fst
diff --git a/detectors/cds/test/test.db/ccsa.fst b/detectors/cds/test/test.db/core/ccsa.fst
similarity index 100%
rename from detectors/cds/test/test.db/ccsa.fst
rename to detectors/cds/test/test.db/core/ccsa.fst
diff --git a/detectors/cds/test/test.db/ndha.fst b/detectors/cds/test/test.db/core/ndha.fst
similarity index 100%
rename from detectors/cds/test/test.db/ndha.fst
rename to detectors/cds/test/test.db/core/ndha.fst
diff --git a/detectors/cds/test/test.db/ndhb.fst b/detectors/cds/test/test.db/core/ndhb.fst
similarity index 100%
rename from detectors/cds/test/test.db/ndhb.fst
rename to detectors/cds/test/test.db/core/ndhb.fst
diff --git a/detectors/cds/test/test.db/ndhd.fst b/detectors/cds/test/test.db/core/ndhd.fst
similarity index 100%
rename from detectors/cds/test/test.db/ndhd.fst
rename to detectors/cds/test/test.db/core/ndhd.fst
diff --git a/detectors/cds/test/test.db/ndhe.fst b/detectors/cds/test/test.db/core/ndhe.fst
similarity index 100%
rename from detectors/cds/test/test.db/ndhe.fst
rename to detectors/cds/test/test.db/core/ndhe.fst
diff --git a/detectors/cds/test/test.db/ndhf.fst b/detectors/cds/test/test.db/core/ndhf.fst
similarity index 100%
rename from detectors/cds/test/test.db/ndhf.fst
rename to detectors/cds/test/test.db/core/ndhf.fst
diff --git a/detectors/cds/test/test.db/ndhg.fst b/detectors/cds/test/test.db/core/ndhg.fst
similarity index 100%
rename from detectors/cds/test/test.db/ndhg.fst
rename to detectors/cds/test/test.db/core/ndhg.fst
diff --git a/detectors/cds/test/test.db/ndhh.fst b/detectors/cds/test/test.db/core/ndhh.fst
similarity index 100%
rename from detectors/cds/test/test.db/ndhh.fst
rename to detectors/cds/test/test.db/core/ndhh.fst
diff --git a/detectors/cds/test/test.db/ndhi.fst b/detectors/cds/test/test.db/core/ndhi.fst
similarity index 100%
rename from detectors/cds/test/test.db/ndhi.fst
rename to detectors/cds/test/test.db/core/ndhi.fst
diff --git a/detectors/cds/test/test.db/psac.fst b/detectors/cds/test/test.db/core/psac.fst
similarity index 100%
rename from detectors/cds/test/test.db/psac.fst
rename to detectors/cds/test/test.db/core/psac.fst
diff --git a/detectors/cds/test/test.db/rpl2.fst b/detectors/cds/test/test.db/core/rpl2.fst
similarity index 100%
rename from detectors/cds/test/test.db/rpl2.fst
rename to detectors/cds/test/test.db/core/rpl2.fst
diff --git a/detectors/cds/test/test.db/rpl23.fst b/detectors/cds/test/test.db/core/rpl23.fst
similarity index 100%
rename from detectors/cds/test/test.db/rpl23.fst
rename to detectors/cds/test/test.db/core/rpl23.fst
diff --git a/detectors/cds/test/test.db/rpl32.fst b/detectors/cds/test/test.db/core/rpl32.fst
similarity index 100%
rename from detectors/cds/test/test.db/rpl32.fst
rename to detectors/cds/test/test.db/core/rpl32.fst
diff --git a/detectors/cds/test/test.db/rps15.fst b/detectors/cds/test/test.db/core/rps15.fst
similarity index 100%
rename from detectors/cds/test/test.db/rps15.fst
rename to detectors/cds/test/test.db/core/rps15.fst
diff --git a/detectors/cds/test/test.db/rps7.fst b/detectors/cds/test/test.db/core/rps7.fst
similarity index 100%
rename from detectors/cds/test/test.db/rps7.fst
rename to detectors/cds/test/test.db/core/rps7.fst
diff --git a/detectors/cds/test/test.db/ycf1.fst b/detectors/cds/test/test.db/core/ycf1.fst
similarity index 100%
rename from detectors/cds/test/test.db/ycf1.fst
rename to detectors/cds/test/test.db/core/ycf1.fst
diff --git a/detectors/cds/test/test.db/ycf2.fst b/detectors/cds/test/test.db/core/ycf2.fst
similarity index 100%
rename from detectors/cds/test/test.db/ycf2.fst
rename to detectors/cds/test/test.db/core/ycf2.fst
diff --git a/detectors/cds/test/test.db/models/blosum62.mat b/detectors/cds/test/test.db/models/blosum62.mat
new file mode 100644
index 0000000..37f3f29
--- /dev/null
+++ b/detectors/cds/test/test.db/models/blosum62.mat
@@ -0,0 +1,29 @@
+#
+# blosum62 substitution matrix
+# with larger penalty for stops
+#
+  A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A 4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -50
+R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -50
+N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -50
+D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -50
+C 0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -50
+Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -50
+E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -50
+G 0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -50
+H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -50
+I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -50
+L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -50
+K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -50
+M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -50
+F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -50
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -50
+S 1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -50
+T 0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -50
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -50
+Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -50
+V 0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -50
+B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -50
+Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -50
+X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -50
+* -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 1
diff --git a/detectors/cds/test/test.db/models/splice.none.frq b/detectors/cds/test/test.db/models/splice.none.frq
new file mode 100644
index 0000000..3a1626c
--- /dev/null
+++ b/detectors/cds/test/test.db/models/splice.none.frq
@@ -0,0 +1,6 @@
+# 3'/5' splice null model
+# A C G T
+25 25 25 25
+splice
+25 25 25 25
+# end of 3'/5' splice null model
diff --git a/detectors/cds/test/test.db/models/splice3.default.frq b/detectors/cds/test/test.db/models/splice3.default.frq
new file mode 100644
index 0000000..4ba2d4c
--- /dev/null
+++ b/detectors/cds/test/test.db/models/splice3.default.frq
@@ -0,0 +1,13 @@
+# 3' splice model : default 
+# A C G T
+19 18 27 36 
+36 5 34 25 
+20 7 51 23 
+29 13 14 44 
+splice
+5 2 78 15 
+3 7 15 75 
+4 1 83 12 
+5 51 13 31 
+5 7 79 9 
+53 10 27 11 
diff --git a/detectors/cds/test/test.db/models/splice3.ndha.frq b/detectors/cds/test/test.db/models/splice3.ndha.frq
new file mode 100644
index 0000000..3584fe3
--- /dev/null
+++ b/detectors/cds/test/test.db/models/splice3.ndha.frq
@@ -0,0 +1,13 @@
+# 3' splice model : ndha 
+# A C G T
+1 43 1 56 
+0 57 0 42 
+41 1 2 56 
+57 42 0 1 
+splice
+1 55 42 2 
+0 1 57 42 
+1 1 43 56 
+2 11 56 31 
+1 29 42 28 
+41 1 57 1 
diff --git a/detectors/cds/test/test.db/models/splice3.psba.frq b/detectors/cds/test/test.db/models/splice3.psba.frq
new file mode 100644
index 0000000..21a6d8a
--- /dev/null
+++ b/detectors/cds/test/test.db/models/splice3.psba.frq
@@ -0,0 +1,13 @@
+# 3' splice model : psba 
+# A C G T
+26 14 40 21 
+13 44 35 9 
+41 3 33 23 
+1 13 5 81 
+splice
+37 5 27 31 
+62 5 9 24 
+56 13 23 8 
+32 28 6 33 
+35 21 17 28 
+53 12 10 26 
diff --git a/detectors/cds/test/test.db/models/splice5.default.frq b/detectors/cds/test/test.db/models/splice5.default.frq
new file mode 100644
index 0000000..b5cb067
--- /dev/null
+++ b/detectors/cds/test/test.db/models/splice5.default.frq
@@ -0,0 +1,13 @@
+# 5' splice model : default 
+# A C G T
+15 42 3 40 
+15 46 6 33 
+13 32 2 53 
+45 17 21 16 
+70 13 6 11 
+21 39 8 32 
+splice
+37 27 9 26 
+31 35 17 17 
+29 23 26 22 
+30 25 28 17 
diff --git a/detectors/cds/test/test.db/models/splice5.ndha.frq b/detectors/cds/test/test.db/models/splice5.ndha.frq
new file mode 100644
index 0000000..fdad60d
--- /dev/null
+++ b/detectors/cds/test/test.db/models/splice5.ndha.frq
@@ -0,0 +1,13 @@
+# 5' splice model : ndha 
+# A C G T
+0 54 2 44 
+43 1 1 56 
+57 1 7 35 
+8 1 39 52 
+56 2 40 2 
+55 1 0 44 
+splice
+1 0 2 97 
+40 1 1 58 
+55 0 1 44 
+1 41 1 58 
diff --git a/detectors/cds/test/test.db/models/splice5.psba.frq b/detectors/cds/test/test.db/models/splice5.psba.frq
new file mode 100644
index 0000000..7785836
--- /dev/null
+++ b/detectors/cds/test/test.db/models/splice5.psba.frq
@@ -0,0 +1,13 @@
+# 5' splice model : psba 
+# A C G T
+38 15 9 37 
+40 5 13 42 
+41 15 6 37 
+32 9 15 44 
+22 8 10 60 
+0 9 83 8 
+splice
+33 15 27 24 
+31 6 26 37 
+17 28 6 49 
+13 15 23 49 
diff --git a/detectors/cds/test/test.db/models/start.default.frq b/detectors/cds/test/test.db/models/start.default.frq
new file mode 100644
index 0000000..aa16582
--- /dev/null
+++ b/detectors/cds/test/test.db/models/start.default.frq
@@ -0,0 +1,8 @@
+# start model : default 
+atg 0.9692592 36165 
+acg 0.01173885 438 
+gtg 0.007504288 280 
+ata 0.003886149 145 
+atc 0.00337693 126 
+att 0.002840909 106 
+ttg 0.001393654 52 
diff --git a/detectors/cds/test/test.db/models/start.ndhd.frq b/detectors/cds/test/test.db/models/start.ndhd.frq
new file mode 100644
index 0000000..893232b
--- /dev/null
+++ b/detectors/cds/test/test.db/models/start.ndhd.frq
@@ -0,0 +1,7 @@
+# start model : ndhd 
+acg 0.5066667 190 
+atg 0.3493333 131 
+atc 0.05066667 19 
+ata 0.03466667 13 
+acc 0.02933333 11 
+gtg 0.02933333 11 
diff --git a/detectors/cds/test/test.db/models/start.rps19.frq b/detectors/cds/test/test.db/models/start.rps19.frq
new file mode 100644
index 0000000..59a3169
--- /dev/null
+++ b/detectors/cds/test/test.db/models/start.rps19.frq
@@ -0,0 +1,3 @@
+# start model : rps19 
+gtg 0.6261023 355 
+atg 0.3738977 212 
diff --git a/detectors/cds/test/test.db/models/stop.default.frq b/detectors/cds/test/test.db/models/stop.default.frq
new file mode 100644
index 0000000..f5f76e5
--- /dev/null
+++ b/detectors/cds/test/test.db/models/stop.default.frq
@@ -0,0 +1,4 @@
+# stop model : default (freq. ignored)
+taa 0.5742367 21968 
+tag 0.2351265 8995 
+tga 0.1906368 7293 
diff --git a/detectors/cds/test/test.ref b/detectors/cds/test/test.ref
index 4101ab6..ba758bd 100644
--- a/detectors/cds/test/test.ref
+++ b/detectors/cds/test/test.ref
@@ -8,6 +8,7 @@ FT                   /gene="ccsA"
 FT                   /locus_tag=""
 FT                   /product="cytochrome c biogenesis protein"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp084"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MIFSTLEHILTHISFSIVSIVITIHLITFLVDEIVKLYDSSEKGI
 FT                   IVTFFCITGLLVTRWVSSGHFPLSDLYESLIFLSWSFSLIHIIPYFKKNVLILSKITGP
 FT                   SAILTQGFATSGILTEIHQSGILVPALQSEWLIMHVSMMILGYAALLCGSLLSVALLVI
@@ -24,6 +25,7 @@ FT                   /gene="ndhA_1"
 FT                   /locus_tag=""
 FT                   /product="NADH dehydrogenase subunit 1"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp085"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="LSNSLSTVDIVEAQSKYGFWGWNLWRQPIGFIVFLISSLAECERL
 FT                   PFDLPEAEEELVAGYQTEYSGIKFGLFYIASYLNLLVSSLFVTVLYLGGWNLSIPYIFV
 FT                   PDIFGINKGGKVFGTLIGIFITLAKTYLFLFIPIATRWTLPRLRMDQLLNLGWKFLLPI
@@ -38,6 +40,7 @@ FT                   /gene="ndhA_2"
 FT                   /locus_tag=""
 FT                   /product="NADH dehydrogenase subunit 1"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp085"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MIIDTTEIETINSFSKLESLKEVYGIIWMLVPIVTLVLGITIGVL
 FT                   VIVWLEREISAGIQQRIGPEYAGPLGILQALADGTKLLLKENLIPSTGDTRLFSIGPSI
 FT                   AVISIFLSYSVIPFGDHLVLADLSIGVFFWIAISSIAPVGLLMSGYGSNNKYSFLGGLR
@@ -52,6 +55,7 @@ FT                   /gene="ndhB"
 FT                   /locus_tag=""
 FT                   /product="NADH dehydrogenase subunit 2"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp066"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MIWHVQNENFILDSTRIFMKAFHLLLFDGSLIFPECILIFGLILL
 FT                   LMIDSTSDQKDIPWLYFISSTSLVMSITALLFRWREEPMISFSGNFQTNNFNEIFQFLI
 FT                   LLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLITIFVAPECFSLCS
@@ -79,6 +83,7 @@ FT                   /gene="ndhD"
 FT                   /locus_tag=""
 FT                   /product="NADH dehydrogenase subunit 4"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp081"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MNYFPWLTIIVVFPIFAGSLIFFLPHKGNRVIRWYTICICILELL
 FT                   LTTYAFCYHFQSDDPLIQLVEDYKWIDFFDFHWRLGIDGLSIGPILLTGFITTLATLAA
 FT                   WPVTRDSRLFHFLMLAMYSGQIGLFSSRDLLLFFIMWELELIPVYLLLAMWGGKKRLYS
@@ -98,6 +103,7 @@ FT                   /gene="ndhE"
 FT                   /locus_tag=""
 FT                   /product="NADH dehydrogenase subunit 4L"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp080"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNAVNINF
 FT                   VTFSDFFDNRQLKGDIFSIFVIAIAAAEAAIGLAIVSSIYRNRKSTRINQSNLLNN"
 FT   gene            complement(11509..13722)
@@ -110,6 +116,7 @@ FT                   /gene="ndhF"
 FT                   /locus_tag=""
 FT                   /product="NADH dehydrogenase subunit 5"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp073"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MEQTYEYAWIIPFIPLPVPMLIGAGLILFPTATKRFRRMWAFQSV
 FT                   LLLSIVMIFSIYLSIQQINSSSVYQYVWSWIINNDFSLDFGYLIDPLTSIMSILITTVG
 FT                   IMVLIYSDNYMAHDQGYLRFFAYMSFFSTSMLGLVTSSNLIQIYIFWELVGLCSYLLIG
@@ -133,6 +140,7 @@ FT                   /gene="ndhG"
 FT                   /locus_tag=""
 FT                   /product="NADH dehydrogenase subunit 6"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp077"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MDLSEPIHDFLLVFLGSGLILGGLGVVLLPNPIYSAFSLGLVLVC
 FT                   TSLFYILSNAYFVAAAQLLIYVGAINVLIIFAVMFMNGSEYYKDFHLWTVGDGITSMVC
 FT                   ISLFISLITTISDTSWYGIIWTTRSNQIIEQDFLSNSQQIGIHLSTDFFLPFELISIIL
@@ -147,6 +155,7 @@ FT                   /gene="ndhH"
 FT                   /locus_tag=""
 FT                   /product="NADH dehydrogenase subunit 7"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp078"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MTAPTTRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVVDCEPILG
 FT                   YLHRGMEKIAENRTIIQYLPYVTRWDYLATMFTEAITINGPEQLGNIQVPKRASYIRVI
 FT                   MLELSRIASHLLWLGPFMADIGAQTPFFYIFRERELIYDLFEAATGMRMMHNYFRIGGV
@@ -164,6 +173,7 @@ FT                   /gene="ndhI"
 FT                   /locus_tag=""
 FT                   /product="NADH dehydrogenase subunit I"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp076"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MLPMITEFINYGQQTIRAARYIGQGFMITLSHANRLPVTIQYPYE
 FT                   KLITSERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETDIRKKRLLNYSIDFGIC
 FT                   IFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALGRLPMSVIDDYTIRTISNLPQ
@@ -178,6 +188,7 @@ FT                   /gene="psaC"
 FT                   /locus_tag=""
 FT                   /product="photosystem I subunit VII"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp065"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRT
 FT                   EDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY"
 FT   gene            53817..55307
@@ -190,6 +201,7 @@ FT                   /gene="rpl2"
 FT                   /locus_tag=""
 FT                   /product="ribosomal protein L2"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp030"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MAIHLYKTSTPSTRNGTVDSQVKSNPRNNLIYGQRRCGKGRNARG
 FT                   IITARHRGGGHKRLYRKIDFRRNEKDIYGRIVTIEYDPNRNAYICLIHYGDGEKRYILH
 FT                   PRGAIIGDTIVSGTEVPIKMGNALPSTDMPLGTAIHNIEITLGKGGQLARAAGAVAKLI
@@ -213,6 +225,7 @@ FT                   /gene="rpl23"
 FT                   /locus_tag=""
 FT                   /product="ribosomal protein L23"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp026"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MDGIKYAVFTDKSIRLLGKNQYTSNVESGSTRTEIKHWVELFFGV
 FT                   KVIAMNSHRLPGKSRRMGPIMGHTMHYRRMIITLQPGYSIPPLRKKRT"
 FT   gene            14505..14672
@@ -225,6 +238,7 @@ FT                   /gene="rpl32"
 FT                   /locus_tag=""
 FT                   /product="ribosomal protein L32"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp036"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MAVPKKRTSTSKKRIRKNIWKRKGYWVALKAFSLAKSLSTGNSKS
 FT                   FFVRQTKINK"
 FT   gene            complement(24633..24896)
@@ -237,6 +251,7 @@ FT                   /gene="rps15"
 FT                   /locus_tag=""
 FT                   /product="ribosomal protein S15"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp029"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MVKNSVISVISQEEKKGSVEFQVFNFTNKIRRLTSHLELHKKDYL
 FT                   SQRGLKKILGKRQRLLAYLAKKNRVRYKELINRLDIRETKTR"
 FT   gene            42157..42624
@@ -249,6 +264,7 @@ FT                   /gene="rps7"
 FT                   /locus_tag=""
 FT                   /product="ribosomal protein S7"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp008"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MSRRGTAEKKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYR
 FT                   AVKKIQQKTETNPLSVLRQAIRGVTPDITVKARRVGGSTHQVPIEIGSTQGKALAIRWL
 FT                   LAASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRAFAHFR"
@@ -262,6 +278,7 @@ FT                   /gene="ycf1"
 FT                   /locus_tag=""
 FT                   /product="hypothetical chloroplast RF1"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp019"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MIFQSFLLGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLL
 FT                   RALVMEEGTEKKVSATTGFITGQLMMFISIYYAPLHLALGRPHTITVLALPYLLFHFFW
 FT                   NNHKHFFDYGSTTRNSMRNLSIQCVFLNNLIFQLFNHFILPSSMLARLVNIYLFRCNNK
@@ -305,6 +322,7 @@ FT                   /gene="ycf2"
 FT                   /locus_tag=""
 FT                   /product="Ycf2"
 FT                   /inference="similar to DNA sequence:AC_000188:LyesCp004"
+FT                   /inference="detect pass:pass1:core"
 FT                   /translation="MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFH
 FT                   QERFLKLFDPRIWSILLSRNSQGSPSNRYFTIKGVILFVVAVLIYRINNRNMVERKNLY
 FT                   LIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKISESCFLNPKESTWVL
diff --git a/scripts/csh_init.sh b/scripts/csh_init.sh
index a19a362..93433eb 100644
--- a/scripts/csh_init.sh
+++ b/scripts/csh_init.sh
@@ -178,4 +178,4 @@ end
 # notification for debug
 # --------------------------------------
 
-Debug "---> $0"
+Debug "---> $0 $argv"