cds go_test bug fixed
Former-commit-id: f73133dca83d02a0c223e98a3ac82fdb0d03c5ae Former-commit-id: 3db7c0037f7c109f4479490480d4323a55206c6a
This commit is contained in:
alain viari
@ -15,47 +15,66 @@
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#
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#========================================================================================
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#
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# usage: do_exonerate.sh dna.fasta prot.fasta [outdir]
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# usage: do_exonerate.sh dna.fasta prot.fasta [model_dir [out_dir]]
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#
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unsetenv ORG_SOURCED
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setenv ORG_HOME `dirname $0`/../../..
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source $ORG_HOME/scripts/csh_init.sh
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set PARAMS_DIR = $LIB_DIR/../params
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set MODELS_DIR = $LIB_DIR/../models
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alias Override 'if (-e \!:2) set \!:1 = \!:2'
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NeedArg 2
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set GenoFile = $Argv[1]
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set GenoFile = $Argv[1]; Shift
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set GenoName = `basename $GenoFile:r`
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set ProtFile = $Argv[2]
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set ProtFile = $Argv[1]; Shift
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set ProtDir = `dirname $ProtFile`
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set ProtName = `basename $ProtFile:r`
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set ProtType = `basename $ProtDir`
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NeedFile $GenoFile
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NeedFile $ProtFile
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NeedFile $ProtDir/Annot.lst
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set ModelsDir = $PROG_DIR/../models
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if ($#Argv > 0) then
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set ModelsDir = $Argv[1]; Shift
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Notify " exonerate models : $ModelsDir"
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else
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Warning " using default exonerate models : $ModelsDir"
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endif
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NeedFile $ModelsDir/start.default.frq
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NeedFile $ModelsDir/stop.default.frq
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NeedFile $ModelsDir/splice3.default.frq
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NeedFile $ModelsDir/splice5.default.frq
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set OutDir = .
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if ($#Argv >= 3) set OutDir = $3
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if ($#Argv > 0) then
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set OutDir = $Argv[1]; Shift
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endif
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if (! -d $OutDir) mkdir $OutDir
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set ParamsDir = $PROG_DIR/../params
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NeedFile $ParamsDir/default
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#
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# general parameters
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#
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source $PARAMS_DIR/default
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source $ParamsDir/default
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#
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# family specific parameters
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#
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if (-e $PARAMS_DIR/$ProtName) then
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source $PARAMS_DIR/$ProtName
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if (-e $ParamsDir/$ProtName) then
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Notify " override parameters with $ParamsDir/$ProtName"
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source $ParamsDir/$ProtName
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endif
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#
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@ -63,23 +82,23 @@ endif
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#
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if ($?STARTMODEL == 0) then
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set STARTMODEL = $MODELS_DIR/start.default.frq
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Override STARTMODEL $MODELS_DIR/start.$ProtName.frq
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set STARTMODEL = $ModelsDir/start.default.frq
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Override STARTMODEL $ModelsDir/start.$ProtName.frq
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endif
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if ($?STOPMODEL == 0) then
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set STOPMODEL = $MODELS_DIR/stop.default.frq
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Override STOPMODEL $MODELS_DIR/stop.$ProtName.frq
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set STOPMODEL = $ModelsDir/stop.default.frq
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Override STOPMODEL $ModelsDir/stop.$ProtName.frq
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endif
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if ($?SPLICE3MODEL == 0) then
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set SPLICE3MODEL = $MODELS_DIR/splice3.default.frq
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Override SPLICE3MODEL $MODELS_DIR/splice3.$ProtName.frq
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set SPLICE3MODEL = $ModelsDir/splice3.default.frq
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Override SPLICE3MODEL $ModelsDir/splice3.$ProtName.frq
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endif
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if ($?SPLICE5MODEL == 0) then
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set SPLICE5MODEL = $MODELS_DIR/splice5.default.frq
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Override SPLICE5MODEL $MODELS_DIR/splice5.$ProtName.frq
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set SPLICE5MODEL = $ModelsDir/splice5.default.frq
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Override SPLICE5MODEL $ModelsDir/splice5.$ProtName.frq
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endif
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#
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@ -178,8 +197,10 @@ $AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \
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# translate
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#
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echo "c pass pass1 $ProtType" > $base.iff
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$AwkCmd -v FASTA=$GenoFile -f $LIB_DIR/libutil.awk \
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-f $LIB_DIR/translate.awk T_$$ > $base.iff
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-f $LIB_DIR/translate.awk T_$$ >> $base.iff
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#
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# convert to embl
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@ -13,7 +13,7 @@
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# Results are printed to the standard output
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#
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#========================================================================================
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# usage: go_cds.sh fasta [db_core]
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# usage: go_cds.sh fasta [db_root]
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#
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unsetenv ORG_SOURCED
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@ -28,13 +28,16 @@ NeedFile $Fasta
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set Genome = `basename $Fasta:r`
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set DbCore = $CDS_DATA_DIR/chlorodb/core
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set DbRoot = $CDS_DATA_DIR/chlorodb
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if ($#Argv > 0) then
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set DbCore = $Argv[1]; Shift
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set DbRoot = $Argv[1]; Shift
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endif
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NeedFile $DbCore/Annot.lst
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NeedDir $DbRoot/core
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NeedFile $DbRoot/core/Annot.lst
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NeedDir $DbRoot/models
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#
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# run everything into temporary place
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@ -50,15 +53,16 @@ endif
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# pass1: run exonerate
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#
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set fams = `ls $DbCore/*.fst`
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Notify "running pass1: exonerate of $Genome on $DbCore"
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foreach f ($fams)
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$PROG_DIR/do_exonerate.sh $Fasta $f $temp
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foreach dir ("core" "shell" "dust")
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if (-d $DbRoot/$dir) then
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set fams = `ls $DbRoot/$dir/*.fst`
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Notify "running pass1:$dir exonerate of $Genome on $DbRoot"
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foreach f ($fams)
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$PROG_DIR/do_exonerate.sh $Fasta $f $DbRoot/models $temp
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end
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endif
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end
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#
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# pass2: transsplicing
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#
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@ -67,10 +67,20 @@ function QQualifier(qual, val) {
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SQualifier(qual, "\"" val "\"")
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}
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function Unk(s) {
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return (s =="" ? "none" : s)
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}
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#
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# rules
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#
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/^c pass/ {
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PassType = $3
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PassInfo = $NF
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next
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}
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/^c annot/ {
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GeneName = $4
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Product = $NF
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@ -113,6 +123,9 @@ function QQualifier(qual, val) {
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/^c end_entry/ {
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GeneName = Unk(GeneName)
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PassType = Unk(PassType)
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gname = (Ngene == 1 ? GeneName : GeneName "_" ++Igene)
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locus = ""
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@ -127,6 +140,7 @@ function QQualifier(qual, val) {
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QQualifier("locus_tag", locus)
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QQualifier("product", Product)
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QQualifier("inference", "similar to DNA sequence:" Simil)
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QQualifier("inference", "detect pass:" PassType ":" PassInfo)
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QQualifier("translation", Translat)
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if (Nexon > 1) {
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@ -2,9 +2,11 @@
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# CDS Searching parameters
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#
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Notify " using default exonerate parameters"
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#
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# general parameters
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# (may be overriden by enviroment variables)
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# may be overriden by enviroment variables (AssignUndef)
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#
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AssignUndef TMP_CLEANUP 1
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@ -30,11 +32,11 @@ AssignUndef PASS1_BESTN 10
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AssignUndef PASS1_FRAMESHIFT -100
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# pass1: exonerate use Blosum62 with larger penalty for Stops
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AssignUndef PASS1_SUBMAT $MODELS_DIR/blosum62.mat
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AssignUndef PASS1_SUBMAT $ModelsDir/blosum62.mat
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# comment next lines to use default or specific splice model
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# AssignUndef SPLICE3MODEL $MODELS_DIR/splice.none.frq
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# AssignUndef SPLICE5MODEL $MODELS_DIR/splice.none.frq
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# AssignUndef SPLICE3MODEL $ModelsDir/splice.none.frq
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# AssignUndef SPLICE5MODEL $ModelsDir/splice.none.frq
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#
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# pass1: cluster selection parameters
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@ -1,6 +1,6 @@
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#!/bin/csh -f
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setenv Verbose 1
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setenv Verbose 0
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setenv ORG_HOME `dirname $0`/../../..
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source $ORG_HOME/scripts/csh_init.sh
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@ -20,7 +20,7 @@ set stat = $status
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if ($stat == 0) then
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echo "+ $VTC[3]CDS test Ok$VTC[1]"
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\rm -r test.bak test.tmp test.db/*.fst.p??
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\rm -r test.bak test.tmp test.db/core/*.fst.p??
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else
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echo "* $VTC[2]CDS test Failure$VTC[1]"
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endif
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29
detectors/cds/test/test.db/models/blosum62.mat
Normal file
29
detectors/cds/test/test.db/models/blosum62.mat
Normal file
@ -0,0 +1,29 @@
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#
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# blosum62 substitution matrix
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# with larger penalty for stops
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#
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A R N D C Q E G H I L K M F P S T W Y V B Z X *
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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* -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 -50 1
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6
detectors/cds/test/test.db/models/splice.none.frq
Normal file
6
detectors/cds/test/test.db/models/splice.none.frq
Normal file
@ -0,0 +1,6 @@
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# 3'/5' splice null model
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# A C G T
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25 25 25 25
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splice
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25 25 25 25
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# end of 3'/5' splice null model
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13
detectors/cds/test/test.db/models/splice3.default.frq
Normal file
13
detectors/cds/test/test.db/models/splice3.default.frq
Normal file
@ -0,0 +1,13 @@
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# 3' splice model : default
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# A C G T
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19 18 27 36
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36 5 34 25
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20 7 51 23
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29 13 14 44
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splice
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5 2 78 15
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3 7 15 75
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4 1 83 12
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5 51 13 31
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5 7 79 9
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53 10 27 11
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13
detectors/cds/test/test.db/models/splice3.ndha.frq
Normal file
13
detectors/cds/test/test.db/models/splice3.ndha.frq
Normal file
@ -0,0 +1,13 @@
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# 3' splice model : ndha
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# A C G T
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1 43 1 56
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0 57 0 42
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41 1 2 56
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57 42 0 1
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splice
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1 55 42 2
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0 1 57 42
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1 1 43 56
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2 11 56 31
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1 29 42 28
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41 1 57 1
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13
detectors/cds/test/test.db/models/splice3.psba.frq
Normal file
13
detectors/cds/test/test.db/models/splice3.psba.frq
Normal file
@ -0,0 +1,13 @@
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# 3' splice model : psba
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# A C G T
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26 14 40 21
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13 44 35 9
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41 3 33 23
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1 13 5 81
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splice
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37 5 27 31
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62 5 9 24
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56 13 23 8
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32 28 6 33
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35 21 17 28
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53 12 10 26
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13
detectors/cds/test/test.db/models/splice5.default.frq
Normal file
13
detectors/cds/test/test.db/models/splice5.default.frq
Normal file
@ -0,0 +1,13 @@
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# 5' splice model : default
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# A C G T
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15 42 3 40
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15 46 6 33
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13 32 2 53
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45 17 21 16
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70 13 6 11
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21 39 8 32
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splice
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37 27 9 26
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31 35 17 17
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29 23 26 22
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30 25 28 17
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13
detectors/cds/test/test.db/models/splice5.ndha.frq
Normal file
13
detectors/cds/test/test.db/models/splice5.ndha.frq
Normal file
@ -0,0 +1,13 @@
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# 5' splice model : ndha
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# A C G T
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0 54 2 44
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43 1 1 56
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57 1 7 35
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8 1 39 52
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56 2 40 2
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55 1 0 44
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splice
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1 0 2 97
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40 1 1 58
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55 0 1 44
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1 41 1 58
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13
detectors/cds/test/test.db/models/splice5.psba.frq
Normal file
13
detectors/cds/test/test.db/models/splice5.psba.frq
Normal file
@ -0,0 +1,13 @@
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# 5' splice model : psba
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# A C G T
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38 15 9 37
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40 5 13 42
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41 15 6 37
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32 9 15 44
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22 8 10 60
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0 9 83 8
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splice
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33 15 27 24
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31 6 26 37
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17 28 6 49
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13 15 23 49
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8
detectors/cds/test/test.db/models/start.default.frq
Normal file
8
detectors/cds/test/test.db/models/start.default.frq
Normal file
@ -0,0 +1,8 @@
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# start model : default
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atg 0.9692592 36165
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acg 0.01173885 438
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gtg 0.007504288 280
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ata 0.003886149 145
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atc 0.00337693 126
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att 0.002840909 106
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ttg 0.001393654 52
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7
detectors/cds/test/test.db/models/start.ndhd.frq
Normal file
7
detectors/cds/test/test.db/models/start.ndhd.frq
Normal file
@ -0,0 +1,7 @@
|
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# start model : ndhd
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acg 0.5066667 190
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||||
atg 0.3493333 131
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atc 0.05066667 19
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ata 0.03466667 13
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acc 0.02933333 11
|
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gtg 0.02933333 11
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3
detectors/cds/test/test.db/models/start.rps19.frq
Normal file
3
detectors/cds/test/test.db/models/start.rps19.frq
Normal file
@ -0,0 +1,3 @@
|
||||
# start model : rps19
|
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gtg 0.6261023 355
|
||||
atg 0.3738977 212
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||||
4
detectors/cds/test/test.db/models/stop.default.frq
Normal file
4
detectors/cds/test/test.db/models/stop.default.frq
Normal file
@ -0,0 +1,4 @@
|
||||
# stop model : default (freq. ignored)
|
||||
taa 0.5742367 21968
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||||
tag 0.2351265 8995
|
||||
tga 0.1906368 7293
|
||||
@ -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
|
||||
|
||||
@ -178,4 +178,4 @@ end
|
||||
# notification for debug
|
||||
# --------------------------------------
|
||||
|
||||
Debug "---> $0"
|
||||
Debug "---> $0 $argv"
|
||||
|
||||
Reference in New Issue
Block a user