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CDS detector added

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Former-commit-id: 93fac7a70052d06c2a12bf8af59820c653edd31b
Former-commit-id: 0869fdad0f550941a0f78f1e4c57f4fcdb3f6076
This commit is contained in:
alain viari
2015-11-08 14:28:05 +01:00
parent 50d5458bc1
commit 8dab2d56b2
648 changed files with 290109 additions and 543 deletions
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78
detectors/cds/bin/go_cds.sh Executable file
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#!/bin/csh -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
#
setenv ORG_HOME `dirname $0`/../../..
source $ORG_HOME/scripts/csh_init.sh
NeedArg 1
set Fasta = $Argv[1]
NeedFile $Fasta
set Genome = `basename $Fasta:r`
NeedFile $CDS_DATA_DIR/chlorodb/core
#
# run everything into temporary place
#
set temp = $Genome.tmp
if (! -d $temp) then
Notify "making directory $temp"
mkdir $temp
endif
#
# pass1: run exonerate
#
set fams = `ls $CDS_DATA_DIR/chlorodb/core/*.fst`
Notify "running pass1: exonerate of $Genome"
foreach f ($fams)
set prot = `basename $f:r`
$LIB_DIR/go_pass1.sh $Fasta $prot $temp
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

131
detectors/cds/lib/bestclust.awk Normal file
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#
# select best cluster(s)
#
# -v MAX_SPAN ALLOW_STOP EXCLUDE
#
BEGIN {
PROCINFO["sorted_in"] = "@ind_num_asc"
if (MAX_SPAN == "") MAX_SPAN = 10000
if (ALLOW_STOP == "") ALLOW_STOP = 0
if (EXCLUDE == "") EXCLUDE = 0
}
/^\# --- START OF GFF DUMP ---/ {
State = "gff"
NbEntry++
next
}
/^\# --- END OF GFF DUMP ---/ {
State = 0
next
}
/^C4 Alignment:/ {
for (i = 1 ; i <= 8 ; i++)
getline
State = "align"
Align = ""
next
}
/^\#/ { next }
(State == 0) { next }
(State == "gff") && ($3 == "gene") {
span = $5 - $4 + 1
valid = (span < MAX_SPAN) \
&& (ALLOW_STOP || (Align !~ "\\*")) \
&& ((EXCLUDE == 0) || (! (Organism ~ EXCLUDE)))
Entry[NbEntry]["valid"] = valid
Entry[NbEntry]["from"] = $4+0
Entry[NbEntry]["to"] = $5+0
Entry[NbEntry]["score"] = $6+0
Entry[NbEntry]["strand"] = $7
if (valid) {
for (i = $4+0 ; i <= $5+0; i++)
Cover[i] = 1
}
}
(State == "gff") && ($3 == "exon") {
Entry[NbEntry]["nbexon"]++
}
(State == "gff") {
n = ++Entry[NbEntry]["nbline"]
$1=$2=""
Entry[NbEntry][n] = $0
}
(State == "align") && /^vulgar/ {
State = 0
split($2, a, "@")
Organism = a[1]
next
}
(State == "align") {
getline; getline
Align = Align "" $0
getline; getline
next
}
END {
# make clusters
pi = -1
for (i in Cover) {
if (i+0 > pi+1)
Clust[++NbClust]["from"] = i
pi = Clust[NbClust]["to"] = i
}
# get highest scoring clusters
for (i = 1 ; i <= NbEntry ; i++) {
valid = Entry[i]["valid"]
if (! valid) continue
clusno = 0
for (j = 1; j <= NbClust; j++) {
if ((Entry[i]["from"] >= Clust[j]["from"]) && (Entry[i]["to"] <= Clust[j]["to"]))
clusno = j
}
valid = (clusno != 0)
if (! valid) continue
score = Entry[i]["score"]
if (score > Clust[clusno]["score"]+0) {
Clust[clusno]["score"] = score
Clust[clusno]["strand"] = Entry[i]["strand"]
Clust[clusno]["entry"] = i
}
}
# print cluster info
print "c nclust", NbClust+0
for (i = 1 ; i <= NbClust ; i++) {
print "c cluster", i, "from", Clust[i]["from"], "to", Clust[i]["to"],\
"strand", Clust[i]["strand"], "score", Clust[i]["score"]
}
# print best clusters
for (i = 1 ; i <= NbClust ; i++) {
if (Clust[i]["score"] == 0) continue
j = Clust[i]["entry"]
s = Clust[i]["strand"]
n = Entry[j]["nbline"]
ne = Entry[j]["nbexon"]
print "c begin_entry", j, "cluster", i, "strand", s, "nbexon", ne
for (k = 1 ; k <= n ; k++) {
entry = Entry[j][k]
gsub("^ +", "", entry)
print "e", entry
}
print "c end_entry", j, "cluster", i
}
}

18
detectors/cds/lib/cutline.awk Normal file
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#
{
line = $0
if (length(line) > 80) {
print substr(line, 1, 80)
rest = substr(line, 81)
while (length(rest) > 59) {
print "FT " substr(rest, 1, 59)
rest = substr(rest, 60)
}
if (length(rest) > 0)
print "FT " rest
}
else {
print line
}
}

135
detectors/cds/lib/extend.awk Normal file
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#
# extend start/stop
#
# -v FASTA START_MODEL STOP_MODEL START_WALK STOP_WALK
#
function UpStart(pos, strand, _local_, seq, i, imax, smax, s) {
seq = Seq
if (strand == "-") {
pos = LenSeq - pos + 1
seq = RevSeq
}
imax = 0
smax = 0
for (i = pos ; i >= Max(1, pos-START_WALK) ; i -= 3) {
s = substr(seq, i, 3)
if (s in StopModel) break
if ((s in StartModel) && (StartModel[s] > smax)) {
imax = i
smax = StartModel[s]
}
}
if (strand == "-") {
imax = (imax > 0) ? LenSeq - imax + 1 : imax
}
return imax
}
#
function DownStop(pos, strand, _local_, seq, i, imax, s) {
seq = Seq
if (strand == "-") {
pos = LenSeq - pos + 1
seq = RevSeq
}
imax = 0
for (i = pos ; i < Min(LenSeq, pos+STOP_WALK) ; i += 3) {
s = substr(seq, i, 3)
if (s in StopModel) {
imax = i
break
}
}
if (strand == "-") {
imax = (imax > 0) ? LenSeq - imax + 1 : imax
}
return imax
}
#
# rules
#
BEGIN {
if (START_MODEL == "") START_MODEL="Models/start.default.frq"
if (STOP_MODEL == "") STOP_MODEL="Models/stop.default.frq"
if (START_WALK == "") START_WALK=120
if (STOP_WALK == "") STOP_WALK=-1
if (! TestPath(FASTA)) Error("Fasta file: '" FASTA "' not found", 1)
Seq = ReadFasta(FASTA)
LenSeq = length(Seq)
RevSeq = RevComplement(Seq)
if (START_WALK < 0) START_WALK = LenSeq
if (STOP_WALK < 0) STOP_WALK = LenSeq
if (! TestPath(START_MODEL)) Error("model file: '" START_MODEL "' not found", 2)
if (! TestPath(STOP_MODEL)) Error("model file: '" STOP_MODEL "' not found", 2)
ReadModel(START_MODEL, StartModel)
ReadModel(STOP_MODEL, StopModel)
}
#
/^c begin_entry/ {
Strand = $7
nbexon = $9+0
StartExon = 1 # always first (even on - strand)
StopExon = nbexon # always last (even on - strand)
NbExon = 0
}
/^c/ {
print $0
next
}
/^e exon/ {
NbExon++
if (NbExon == StartExon) {
pos = (Strand == "+" ? $3+0 : $4+0)
start = UpStart(pos, Strand)
mod_start = (start == 0 ? (Strand == "+" ? "<" : ">") : "=")
start = (start == 0 ? pos : start)
$(Strand == "+" ? 3 : 4) = start
} else {
mod_start = "="
}
if (NbExon == StopExon) {
pos = (Strand == "+" ? $4+0 : $3+0)
pos += (Strand == "+" ? 1 : -1)
stop = DownStop(pos, Strand)
mod_stop = (stop == 0 ? (Strand == "+" ? ">" : "<") : "=")
last = (stop == 0 ? pos : stop)
last += (Strand == "+" ? -1 : 1)
stop = last + (stop == 0 ? 0 : (Strand == "+") ? 3 : -3)
$(Strand == "+" ? 4 : 3) = stop
} else {
mod_stop = "="
}
modif = (Strand == "+" ? mod_start "" mod_stop : mod_stop "" mod_start)
print $0, "; modifier \"" modif "\""
next
}
/^e (intron|splice|similarity)/ {
print $0
next
}

27
detectors/cds/lib/filterbx.awk Normal file
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#
#
# filter BlastX results for speedup
#
BEGIN {
if (IDMIN == "") IDMIN = 80
if (NBMIN == "") NBMIN = 50
if (NBMAX == "") NBMAX = 200
}
/^#/ { next }
{
if ((($3+0 >= IDMIN) || (HitNum <= NBMIN)) && (HitIndex[$2] == 0)) {
HitIndex[$2] = ++HitNum
IndexHit[HitNum] = $2
}
}
END {
n = (HitNum > NBMAX) ? NBMAX : HitNum
for (i = 1 ; i <= n ; i++)
print IndexHit[i]
}

62
detectors/cds/lib/go_filterbx.sh Executable file
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#!/bin/csh -f
#
# filter a DB thru BlastX
# usually to speedup further DB search
#
# output on stdout
#
# usage: go_filterbx.sh dna_fasta prot_fasta [idmin nbmin nbmax]
#
setenv ORG_HOME `dirname $0`/../../..
source $ORG_HOME/scripts/csh_init.sh
NeedArg 2
set GenoFile = $Argv[1]; Shift
set ProtFile = $Argv[1]; Shift
NeedFile $GenoFile
NeedFile $ProtFile
set IDMIN = 70
set NBMIN = 50
set NBMAX = 200
if ($#Argv >= 1) set IDMIN = $Argv[1]
if ($#Argv >= 2) set NBMIN = $Argv[2]
if ($#Argv >= 3) set NBMAX = $Argv[3]
#
# format ProtFile
#
if (! -e $ProtFile.phr) then
Notify " formatting $ProtFile"
(makeblastdb -dbtype prot -in $ProtFile) >& /dev/null
CheckAbort 10 "makeblastdb failure"
endif
#
# blastx
#
Notify " blasting $ProtFile"
blastx -query $GenoFile -db $ProtFile -outfmt 7 |\
$AwkCmd -v IDMIN=$IDMIN \
-v NBMIN=$NBMIN \
-v NBMAX=$NBMAX \
-f $LIB_DIR/filterbx.awk > T_$$
#
# extract subdb
#
$AwkCmd -v FILE=T_$$ -f $LIB_DIR/subdb.awk $ProtFile
#
# end
#
(\rm -f ?_$$) >> /dev/null
Exit 0

197
detectors/cds/lib/go_pass1.sh Executable file
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#!/bin/csh -f
#
# Annotate CDS - Pass1
#
#========================================================================================
#
# Annotate CDS of chlorodb/core proteins using exonerate
#
# pass1.sh <FASTAFILE> <FAMILY> [<OUTDIR>]
#
# - <FASTAFILE> : The fasta file containing the genome to annotate
# - <FAMILY> : Name of the protein family (defined in chlorodb/core)
#
# Results are in file : `basename <FASTAFILE>:r`.<FAMILY>.res
#
#========================================================================================
#
# usage: go_pass1.sh fasta family [outdir]
#
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 GenoName = `basename $GenoFile:r`
set ProtName = $Argv[2]
set ProtDir = $CDS_DATA_DIR/chlorodb/core
set ProtFile = $ProtDir/$ProtName.fst
NeedFile $GenoFile
NeedFile $ProtFile
set OutDir = .
if ($#Argv >= 3) set OutDir = $3
if (! -d $OutDir) mkdir $OutDir
#
# general parameters
#
source $PARAMS_DIR/default
#
# family specific parameters
#
if (-e $PARAMS_DIR/$ProtName) then
source $PARAMS_DIR/$ProtName
endif
#
# start/stop/splice models
#
if ($?STARTMODEL == 0) then
set STARTMODEL = $MODELS_DIR/start.default.frq
Override STARTMODEL $MODELS_DIR/start.$ProtName.frq
endif
if ($?STOPMODEL == 0) then
set STOPMODEL = $MODELS_DIR/stop.default.frq
Override STOPMODEL $MODELS_DIR/stop.$ProtName.frq
endif
if ($?SPLICE3MODEL == 0) then
set SPLICE3MODEL = $MODELS_DIR/splice3.default.frq
Override SPLICE3MODEL $MODELS_DIR/splice3.$ProtName.frq
endif
if ($?SPLICE5MODEL == 0) then
set SPLICE5MODEL = $MODELS_DIR/splice5.default.frq
Override SPLICE5MODEL $MODELS_DIR/splice5.$ProtName.frq
endif
#
# out files prefix
#
set base = $OutDir/$GenoName.$ProtName
#
# skip exonerate calculations if already done
#
if (-e $base.exo.raw) then
Notify " file $base.exo.raw found <exonerate skipped>"
goto parse
endif
#
# speedup exonerate
#
if ($PASS1_SPEEDUP != 0) then
$LIB_DIR/go_filterbx.sh $GenoFile $ProtFile \
$PASS1_BLASTX_FILTER_IDMIN \
$PASS1_BLASTX_FILTER_NBMIN \
$PASS1_BLASTX_FILTER_NBMAX > D_$$
set n = `egrep "^>" D_$$ | wc -l`
if ($n > 0) then
Notify " $n sequences kept"
set DbFile = D_$$
else
Notify " no sequence match"
if ($PASS1_SLOWDOWN != 0) then
Notify " reverting to original $ProtName"
set DbFile = $ProtFile
else
echo "" > $base.exo.raw
goto parse
endif
endif
else
set DbFile = $ProtFile
endif
#
# run exonerate
#
Notify " running exonerate of $GenoName on $ProtName"
exonerate --model protein2genome \
--percent $PASS1_PERCENT \
--showalignment TRUE \
--showvulgar TRUE \
--showtargetgff TRUE \
--geneticcode $PASS1_GENETIC_CODE \
--minintron $PASS1_MIN_INTRON \
--maxintron $PASS1_MAX_INTRON \
--bestn $PASS1_BESTN \
--frameshift $PASS1_FRAMESHIFT \
--proteinsubmat $PASS1_SUBMAT \
--splice3 $SPLICE3MODEL \
--splice5 $SPLICE5MODEL \
$DbFile $GenoFile > $base.exo.raw
CheckAbort 20 "exonerate failure"
#
# extract best clusters
#
parse:
$AwkCmd -v MAX_SPAN=$PASS1_MAX_SPAN \
-v ALLOW_STOP=$PASS1_ALLOW_STOP \
-v EXCLUDE=$GenoName \
-f $LIB_DIR/bestclust.awk $base.exo.raw > $base.exo.best
#
# get annotations
#
egrep "^$ProtName " $CDS_DATA_DIR/chlorodb/core/Annot.lst |\
awk '{print "c annot", $0}' > T_$$
#
# extend start/stop
#
$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/extend.awk \
-v FASTA=$GenoFile \
-v START_MODEL=$STARTMODEL \
-v STOP_MODEL=$STOPMODEL \
-v START_WALK=$PASS1_START_WALK \
-v STOP_WALK=$PASS1_STOP_WALK \
$base.exo.best >> T_$$
#
# translate
#
$AwkCmd -v FASTA=$GenoFile -f $LIB_DIR/libutil.awk \
-f $LIB_DIR/translate.awk T_$$ > $base.iff
#
# convert to embl
#
$AwkCmd -f $LIB_DIR/toEmbl.awk $base.iff |\
$AwkCmd -f $LIB_DIR/cutline.awk > $base.res
#
# end
#
Notify " output file: $base.res"
(\rm -f ?_$$) >> /dev/null
Exit 0

179
detectors/cds/lib/libutil.awk Normal file
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#
# utilities library
#
END {
if (_ForceExit_) exit(_ForceExit_)
}
function Notify(key, msg) {
print "# " key " " msg >> "/dev/stderr"
}
function Info(msg) {
Notify("info", msg)
return 1
}
function Warning(msg) {
Notify("warning", msg)
return 0
}
function Exit(status) {
exit(_ForceExit_ = status)
}
function Error(msg, status) {
Notify("error", msg)
Exit(status ? status : 1)
}
function Assert(condition, msg, status) {
if (! condition) {
msg = FILENAME ":" FNR ": " msg
return status ? Error(msg, status) : Warning(msg)
}
}
#
function Min(a, b) {
return (a < b ? a : b)
}
function Max(a, b) {
return (a > b ? a : b)
}
#
function Trim(s, regexp) {
if (regexp == 0) regexp = "[ \t]+"
gsub("^" regexp "|" regexp "$", "", s)
return s
}
function ShieldPath(path) {
gsub(" ", "\\ ", path)
return path
}
function TestPath(path, test, _local_, stat) {
if (test == 0) test = "-f"
if (Trim(path) == "")
return 0 # because of a bug in 'test'
stat = system("test " test " " ShieldPath(path))
return stat ? 0 : 1
}
#
function Reverse(s, _local_, i, n, rs) {
rs = "";
n = length(s);
for (i = n ; i >= 1 ; i--)
rs = rs "" substr(s, i, 1)
return rs;
}
function RevComplement(seq, _local_, n, i, c, rs) {
n = length(seq)
rs = ""
for (i = n ; i >= 1 ; i--) {
c = substr(seq, i, 1)
rs = rs "" (_DnaC[c] ? _DnaC[c] : "X")
}
return rs
}
#
function _AssertCode(name, _local_, n, i1, i2, i3, b1, b2, b3) {
if (_InitCod[name] != 0) return 1
for (i1 = 1 ; i1 <= 4 ; i1++) {
b1 = substr(_NucOrder, i1, 1)
for (i2 = 1 ; i2 <= 4 ; i2++) {
b2 = substr(_NucOrder, i2, 1)
for (i3 = 1 ; i3 <= 4 ; i3++) {
b3 = substr(_NucOrder, i3, 1)
_GenCod[name][b1 "" b2 "" b3] = substr(_Cod2Aa[name], ++n, 1)
}
}
}
_InitCod[name] = 1
return 1
}
function Translate(seq, codname, _local_, n, i, c, p) {
if (codname == 0) codname = "universal"
_AssertCode(codname)
seq = toupper(seq)
n = length(seq)
p = ""
for (i = 1 ; i <= n ; i += 3) {
c = substr(seq, i, 3)
p = p "" ((c in _GenCod[codname]) ? _GenCod[codname][c] : "X")
}
return p
}
#
function SubSeq(seq, from, to, revstrand) {
seq = substr(seq, from, to-from+1)
if (revstrand) seq = RevComplement(seq)
return seq
}
#
function ReadFasta(file, _local_, seq, context) {
context = $0
seq = ""
getline < file
while(getline < file) seq = seq "" $0
$0 = context
return seq
}
#
function ReadModel(file, a, _local_, line, context) {
context = $0
delete a
while(getline < file)
if (! ($0 ~ "^#")) a[$1] = $2
$0 = context
}
#
# constants
#
BEGIN {
# complementary of _IupacDna
_DnaC["A"] = "T"; _DnaC["C"] = "G"; _DnaC["G"] = "C"; _DnaC["T"] = "A"
_DnaC["R"] = "Y"; _DnaC["Y"] = "R"; _DnaC["M"] = "K"; _DnaC["K"] = "M"
_DnaC["W"] = "W"; _DnaC["S"] = "S"; _DnaC["B"] = "V"; _DnaC["V"] = "B"
_DnaC["D"] = "H"; _DnaC["H"] = "D"; _DnaC["N"] = "N"; _DnaC["X"] = "X"
_DnaC["a"] = "t"; _DnaC["c"] = "g"; _DnaC["g"] = "c"; _DnaC["t"] = "a"
_DnaC["r"] = "y"; _DnaC["y"] = "r"; _DnaC["m"] = "k"; _DnaC["k"] = "m"
_DnaC["w"] = "w"; _DnaC["s"] = "s"; _DnaC["b"] = "v"; _DnaC["v"] = "b"
_DnaC["d"] = "h"; _DnaC["h"] = "d"; _DnaC["n"] = "n"; _DnaC["x"] = "x"
# genetic codes
_NucOrder = "ACGT"
#1 AAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTT
#2 AAAACCCCGGGGTTTTAAAACCCCGGGGTTTTAAAACCCCGGGGTTTTAAAACCCCGGGGTTTT
#3 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
_Cod2Aa["universal"] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF"
_Cod2Aa["mito-yeast"] = "KNKNTTTTRSRSMIMIQHQHPPPPRRRRTTTTEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"
_Cod2Aa["mito-vertebrates"] = "KNKNTTTT*S*SMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"
_Cod2Aa["mito-insects"] = "KNKNTTTTSSSSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"
_Cod2Aa["mito-echinoderms"] = "NNKNTTTTSSSSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"
_Cod2Aa["mycoplasma"] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"
_Cod2Aa["ciliata"] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVQYQYSSSS*CWCLFLF"
_Cod2Aa["euplotes"] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSCCWCLFLF"
_Cod2Aa["candida"] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRXLSLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF"
}

20
detectors/cds/lib/subdb.awk Normal file
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#
# select subDB from fasta DB
#
# -v FILE
BEGIN {
if (FILE == "") FILE = "dbsel.txt"
while (getline < FILE)
INC[$1] = $1
close(FILE)
}
/^>/ {
name = substr($1, 2)
ok = name in INC
}
ok {
print $0
}

141
detectors/cds/lib/toEmbl.awk Normal file
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#
# iff -> embl
#
function FromLoc(i, _local_, s) {
s = substr(Exon[i]["modif"], 1, 1) "" Exon[i]["from"]
gsub("=", "", s)
return s
}
function ToLoc(i, _local_, s) {
s = substr(Exon[i]["modif"], 2, 1) "" Exon[i]["to"]
gsub("=", "", s)
return s
}
function GeneLocation(_local_, d, s) {
d = Exon[1]["strand"]
if (d == "+")
s = FromLoc(1) ".." ToLoc(Nexon)
else
s = FromLoc(Nexon) ".." ToLoc(1)
if (d == "-") s = "complement(" s ")"
return s
}
function CdsLocation(_local_, d, i, s) {
d = Exon[1]["strand"]
if (d == "+") {
for (i = 1 ; i <= Nexon ; i++)
s = s "," FromLoc(i) ".." ToLoc(i)
}
else {
for (i = Nexon ; i >= 1 ; i--)
s = s "," FromLoc(i) ".." ToLoc(i)
}
s = substr(s, 2)
if (Nexon > 1) s = "join(" s ")"
if (d == "-") s = "complement(" s ")"
return s
}
function ExonLocation(i, _local_, s) {
s = FromLoc(i) ".." ToLoc(i)
if (Exon[i]["strand"] == "-") s = "complement(" s ")"
return s
}
function Pad(s, len) {
while (length(s) < len)
s = s " "
return s
}
function Feature(feat, loc, _local_, s) {
s = Pad("FT " feat, 21)
print s "" loc
}
function SQualifier(qual, val, _local_, s) {
s = Pad("FT", 21)
print s "/" qual "=" val
}
function QQualifier(qual, val) {
SQualifier(qual, "\"" val "\"")
}
#
# rules
#
/^c annot/ {
GeneName = $4
Product = $NF
gsub("_", " ", Product)
next
}
/^c nclust/ {
Ngene = $3
next
}
/^c begin_entry/ {
Nexon = 0
delete Exon
next
}
/^e exon/ {
Nexon++
Exon[Nexon]["from"] = $3
Exon[Nexon]["to"] = $4
Exon[Nexon]["strand"] = $6
Exon[Nexon]["indels"] = $9 "+" $12
modif = $15; gsub("\"", "", modif)
Exon[Nexon]["modif"] = modif
next
}
/^e similarity/ {
split($12, a, "@")
Simil = a[1] ":" a[2]
next
}
/^e translate/ {
Translat = $3
next
}
/^c end_entry/ {
gname = (Ngene == 1 ? GeneName : GeneName "_" ++Igene)
locus = ""
Feature("gene", GeneLocation())
QQualifier("gene", gname)
QQualifier("locus_tag", locus)
Feature("CDS", CdsLocation())
SQualifier("codon_start", 1)
SQualifier("transl_table", 11)
QQualifier("gene", gname)
QQualifier("locus_tag", locus)
SQualifier("product", Product)
QQualifier("inference", "similar to DNA sequence:" Simil)
QQualifier("translation", Translat)
if (Nexon > 1) {
for (i = 1 ; i <= Nexon ; i++) {
Feature("exon", ExonLocation(i))
QQualifier("gene", gname)
QQualifier("locus_tag", locus)
SQualifier("number", Exon[1]["strand"] == "+" ? i : Nexon-i+1)
}
}
}

39
detectors/cds/lib/translate.awk Normal file
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#
# translate CDSs from iff file
#
BEGIN {
Seq = ReadFasta(FASTA)
}
/^c end_entry/ {
if (RevStrand) Cds = RevComplement(Cds)
Prot = Translate(substr(Cds, 1, length(Cds)-3))
if (Modif == "=")
Prot = "M" substr(Prot, 2)
print "e translate " Prot
}
{
print $0
}
/^c begin_entry/ {
Cds = ""
Iexon = 0
next
}
/^e exon/ {
RevStrand = ($6 == "-")
if (++Iexon == 1) { # first is exon with start (even on - strand)
Modif = $15
gsub("\"", "", Modif)
Modif = (RevStrand ? substr(Modif, 2, 1) : substr(Modif, 1, 1))
}
if (RevStrand)
Cds = SubSeq(Seq, $3, $4) "" Cds
else
Cds = Cds "" SubSeq(Seq, $3, $4)
next
}

29
detectors/cds/models/blosum62.mat Normal file
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#
# 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

6
detectors/cds/models/splice.none.frq Normal file
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# 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

13
detectors/cds/models/splice3.default.frq Normal file
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# 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

13
detectors/cds/models/splice3.ndha.frq Normal file
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# 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

13
detectors/cds/models/splice3.psba.frq Normal file
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# 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

13
detectors/cds/models/splice5.default.frq Normal file
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# 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

13
detectors/cds/models/splice5.ndha.frq Normal file
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# 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

13
detectors/cds/models/splice5.psba.frq Normal file
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@ -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

8
detectors/cds/models/start.default.frq Normal file
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# 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

7
detectors/cds/models/start.ndhd.frq Normal file
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# 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

3
detectors/cds/models/start.rps19.frq Normal file
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# start model : rps19
gtg 0.6261023 355
atg 0.3738977 212

4
detectors/cds/models/stop.default.frq Normal file
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# stop model : default (freq. ignored)
taa 0.5742367 21968
tag 0.2351265 8995
tga 0.1906368 7293

50
detectors/cds/params/default Normal file
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#
# CDS Searching parameters
#
#
# general parameters
# (may be overriden by enviroment variables)
#
AssignUndef TMP_CLEANUP 1
#
# pass1: exonerate speedup
#
AssignUndef PASS1_SPEEDUP 1
AssignUndef PASS1_SLOWDOWN 0
AssignUndef PASS1_BLASTX_FILTER_IDMIN 70
AssignUndef PASS1_BLASTX_FILTER_NBMIN 50
AssignUndef PASS1_BLASTX_FILTER_NBMAX 200
#
# pass1: exonerate parameters
#
AssignUndef PASS1_PERCENT 30
AssignUndef PASS1_MIN_INTRON 30
AssignUndef PASS1_MAX_INTRON 6000
AssignUndef PASS1_GENETIC_CODE 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
# comment next lines to use default or specific splice model
# AssignUndef SPLICE3MODEL $MODELS_DIR/splice.none.frq
# AssignUndef SPLICE5MODEL $MODELS_DIR/splice.none.frq
#
# pass1: cluster selection parameters
#
AssignUndef PASS1_MAX_SPAN 10000
AssignUndef PASS1_ALLOW_STOP 0
#
# extension parameters
#
AssignUndef PASS1_START_WALK 120
AssignUndef PASS1_STOP_WALK -1

22
detectors/cds/test/go_test.sh Executable file
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#!/bin/csh -f
echo "+ [testing CDS]"
setenv PASS1_SPEEDUP 1
setenv PASS1_SLOWDOWN 0
setenv PASS1_BLASTX_FILTER_NBMAX 50
../bin/go_cds.sh test.fst > test.bak
diff -q test.bak test.ref >& /dev/null
set stat = $status
if ($stat == 0) then
echo '+ CDS test Ok'
\rm -r test.bak
else
echo '* CDS test Failure'
endif
exit $stat

1111
detectors/cds/test/test.fst Normal file
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File diff suppressed because it is too large Load Diff

347
detectors/cds/test/test.ref Normal file
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FT gene 15766..16707
FT /gene="ccsA"
FT /locus_tag=""
FT CDS 15766..16707
FT /codon_start=1
FT /transl_table=11
FT /gene="ccsA"
FT /locus_tag=""
FT /product=cytochrome c biogenesis protein
FT /inference="similar to DNA sequence:AC_000188:LyesCp084"
FT /translation="MIFSTLEHILTHISFSIVSIVITIHLITFLVDEIVKLYDSSEKGI
FT IVTFFCITGLLVTRWVSSGHFPLSDLYESLIFLSWSFSLIHIIPYFKKNVLILSKITGP
FT SAILTQGFATSGILTEIHQSGILVPALQSEWLIMHVSMMILGYAALLCGSLLSVALLVI
FT TFRKNRKLFSKSNVFLNESFFLGENVVENTSFFCTKNYYRSQLIQQLDYWSYRVISLGF
FT TFLTIGILSGAVWANEAWGSYWNWDPKETWAFITWIVFAIYLHTRTNRNLRGPNSAIVA
FT SIGFLIIWICYFGVNLLGIGLHSYGSFPSTFN"
FT gene complement(21114..>21653)
FT /gene="ndhA_1"
FT /locus_tag=""
FT CDS complement(21114..>21653)
FT /codon_start=1
FT /transl_table=11
FT /gene="ndhA_1"
FT /locus_tag=""
FT /product=NADH dehydrogenase subunit 1
FT /inference="similar to DNA sequence:AC_000188:LyesCp085"
FT /translation="LSNSLSTVDIVEAQSKYGFWGWNLWRQPIGFIVFLISSLAECERL
FT PFDLPEAEEELVAGYQTEYSGIKFGLFYIASYLNLLVSSLFVTVLYLGGWNLSIPYIFV
FT PDIFGINKGGKVFGTLIGIFITLAKTYLFLFIPIATRWTLPRLRMDQLLNLGWKFLLPI
FT SLGNLLLTTSSQLLSL"
FT gene complement(22772..23338)
FT /gene="ndhA_2"
FT /locus_tag=""
FT CDS complement(22772..23338)
FT /codon_start=1
FT /transl_table=11
FT /gene="ndhA_2"
FT /locus_tag=""
FT /product=NADH dehydrogenase subunit 1
FT /inference="similar to DNA sequence:AC_000188:LyesCp085"
FT /translation="MIIDTTEIETINSFSKLESLKEVYGIIWMLVPIVTLVLGITIGVL
FT VIVWLEREISAGIQQRIGPEYAGPLGILQALADGTKLLLKENLIPSTGDTRLFSIGPSI
FT AVISIFLSYSVIPFGDHLVLADLSIGVFFWIAISSIAPVGLLMSGYGSNNKYSFLGGLR
FT AAAQSISYEIPLALCVLSISLRVIR"
FT gene 42910..45121
FT /gene="ndhB"
FT /locus_tag=""
FT CDS join(42910..43780,44367..45121)
FT /codon_start=1
FT /transl_table=11
FT /gene="ndhB"
FT /locus_tag=""
FT /product=NADH dehydrogenase subunit 2
FT /inference="similar to DNA sequence:NC_008535:CoarCp067"
FT /translation="MIWHVQNENFILDSTRIFMKAFHLLLFDGSLIFPECILIFGLILL
FT LMIDSTSDQKDIPWLYFISSTSLVMSITALLFRWREEPMISFSGNFQTNNFNEIFQFLI
FT LLCSTLCIPLSVEYIECTEMAITEFLLFVLTATLGGMFLCGANDLITIFVAPECFSLCS
FT YLLSGYTKKDVRSNEATMKYLLMGGASSSILVHGFSWLYGSSGGEIELQEIVNGLINTQ
FT MYNSPGISIALIFITVGIGFKLSPAPSHQWTPDVYEGVRFVREIPTSLSISEMFGFFKT
FT PWTCRREMLSPTPVVAFLSVTSKVAASASATRIFNIPFYFSSNEWHLLLEILAILSMIL
FT GNLIAITQTSMKRMLAYSSIGQIGYVIIGIIVGDSNDGYASMITYMLFYISMNLGTFAC
FT IVLFGLRTGTDNIRDYAGLYTKDPFLALSLALCLLSLGGLPPLAGFFGKLYLFWCGWQA
FT GLYFLVLIGLLTSVVSIYYYLKIIKLLMTGRNQEITPHVRNYRRSPLRSNNSIELSMIV
FT CVIASTIPGISMNPIIAIAQDSLF"
FT exon 42910..43780
FT /gene="ndhB"
FT /locus_tag=""
FT /number=1
FT exon 44367..45121
FT /gene="ndhB"
FT /locus_tag=""
FT /number=2
FT gene complement(16945..18447)
FT /gene="ndhD"
FT /locus_tag=""
FT CDS complement(16945..18447)
FT /codon_start=1
FT /transl_table=11
FT /gene="ndhD"
FT /locus_tag=""
FT /product=NADH dehydrogenase subunit 4
FT /inference="similar to DNA sequence:NC_007898:LyesC2p017"
FT /translation="MNYFPWLTIIVVFPIFAGSLIFFLPHKGNRVIRWYTICICILELL
FT LTTYAFCYHFQSDDPLIQLVEDYKWIDFFDFHWRLGIDGLSIGPILLTGFITTLATLAA
FT WPVTRDSRLFHFLMLAMYSGQIGLFSSRDLLLFFIMWELELIPVYLLLAMWGGKKRLYS
FT ATKFILYTAGGSVFLLMGVLGVALYGSNEPTLNFETSVNQSYPVVLEIIFYIGFFIAFA
FT VKSPIIPLHTWLPDTHGEAHYSTCMLLAGILLKMGAYGLIRINMELLPHAHSIFSPWLM
FT IIGTIQIIYAASTSLGQRNLKKRIAYSSVSHMGFIIIGISSLTDTGLNGALLQIISHGF
FT IGAALFFLAGTTYDRIRLVYLDEMGGIAIPMPKMFTMFSSFSMASLALPGMSGFVAELI
FT VFFGIITGQKYLLMPKLLITFVMAIGIILTPIYSLSMPRQMFYGYKLFNAPKDSFFDSG
FT PRELFLSISIFLPVIGIGIYPDFVLSLAVDKVEVILSNFFYR"
FT gene complement(19062..19367)
FT /gene="ndhE"
FT /locus_tag=""
FT CDS complement(19062..19367)
FT /codon_start=1
FT /transl_table=11
FT /gene="ndhE"
FT /locus_tag=""
FT /product=NADH dehydrogenase subunit 4L
FT /inference="similar to DNA sequence:AC_000188:LyesCp080"
FT /translation="MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNAVNINF
FT VTFSDFFDNRQLKGDIFSIFVIAIAAAEAAIGLAIVSSIYRNRKSTRINQSNLLNN"
FT gene complement(11509..13722)
FT /gene="ndhF"
FT /locus_tag=""
FT CDS complement(11509..13722)
FT /codon_start=1
FT /transl_table=11
FT /gene="ndhF"
FT /locus_tag=""
FT /product=NADH dehydrogenase subunit 5
FT /inference="similar to DNA sequence:AC_000188:LyesCp073"
FT /translation="MEQTYEYAWIIPFIPLPVPMLIGAGLILFPTATKRFRRMWAFQSV
FT LLLSIVMIFSIYLSIQQINSSSVYQYVWSWIINNDFSLDFGYLIDPLTSIMSILITTVG
FT IMVLIYSDNYMAHDQGYLRFFAYMSFFSTSMLGLVTSSNLIQIYIFWELVGLCSYLLIG
FT FWFTRPVAANACQKAFVTNRVGDFGLLLGILGFYWITGSFEFRDLFEIFNNLIYNNELN
FT FLFVTLCAVLLFAGAVAKSAQFPLHVWLPDAMEGPTPISALIHAATMVAAGIFLVARLL
FT PLFRVIPYIMYLISVIGIITVLLGATLALAQKDIKRGLAYSTMSQLGYMMLALGMGSYR
FT SALFHLITHAYSKALLFLGSGSIIHSMETIVGYSPAKSQNMGLMGGLRKHVPITKITFL
FT LGTLSLCGIPPLACFWSKDEILNDSWLYSPIFAIIAWATAGLTAFYMFRIYLLTFEGHL
FT NAHFQNYGGKQKIPFYSISLWGKNGVKKNSCLLTMNNNESTYFLSKTKYPIAKNGRKMT
FT RPFMTIAHFKHKAVSSYPYESDNTMLFPIFVLGLFTLFVGAIGIPFNQEGVNLDILSKW
FT LAPSINLLHPKSNNSLDWNEFLKDAVVSVSIAYFGIFIASFLYKPIYSSLKNLEFINSF
FT VKKGPKRILWDKILNGIYDWSYNRAYIDAFYTRFFVGGIRGLAEFTHFVDRRVIDGMTN
FT GVGVISFIVGEGIKYIGGGRISSYLFLYLAYVSVFLLVYYLLF"
FT gene complement(19591..20121)
FT /gene="ndhG"
FT /locus_tag=""
FT CDS complement(19591..20121)
FT /codon_start=1
FT /transl_table=11
FT /gene="ndhG"
FT /locus_tag=""
FT /product=NADH dehydrogenase subunit 6
FT /inference="similar to DNA sequence:AC_000188:LyesCp077"
FT /translation="MDLSEPIHDFLLVFLGSGLILGGLGVVLLPNPIYSAFSLGLVLVC
FT TSLFYILSNAYFVAAAQLLIYVGAINVLIIFAVMFMNGSEYYKDFHLWTVGDGITSMVC
FT ISLFISLITTISDTSWYGIIWTTRSNQIIEQDFLSNSQQIGIHLSTDFFLPFELISIIL
FT LVALIGAIAVARQ"
FT gene complement(23340..24521)
FT /gene="ndhH"
FT /locus_tag=""
FT CDS complement(23340..24521)
FT /codon_start=1
FT /transl_table=11
FT /gene="ndhH"
FT /locus_tag=""
FT /product=NADH dehydrogenase subunit 7
FT /inference="similar to DNA sequence:AC_000188:LyesCp078"
FT /translation="MTAPTTRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVVDCEPILG
FT YLHRGMEKIAENRTIIQYLPYVTRWDYLATMFTEAITINGPEQLGNIQVPKRASYIRVI
FT MLELSRIASHLLWLGPFMADIGAQTPFFYIFRERELIYDLFEAATGMRMMHNYFRIGGV
FT AADLPYGWIDKCLDFCDYFLTGVAEYQKLITRNPIFLERVEGVGIIGRDEALNWGLSGP
FT MLRASGIEWDLRKVDHYESYDEFDWQVQWQREGDSLARYLVRIGEMTESIKIIQQALEG
FT IPGGPYENLEMRRFDRLKDPEWNDFEYRFISKKPSPTFELSKQELYVRVEAPKGELGIF
FT LIGDQSVFPWRWKIRPPGFINLQILPQLVKRMKLADIMTILGSIDIIMGEVDR"
FT gene complement(20526..21029)
FT /gene="ndhI"
FT /locus_tag=""
FT CDS complement(20526..21029)
FT /codon_start=1
FT /transl_table=11
FT /gene="ndhI"
FT /locus_tag=""
FT /product=NADH dehydrogenase subunit I
FT /inference="similar to DNA sequence:AC_000188:LyesCp076"
FT /translation="MLPMITEFINYGQQTIRAARYIGQGFMITLSHANRLPVTIQYPYE
FT KLITSERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETDIRKKRLLNYSIDFGIC
FT IFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALGRLPMSVIDDYTIRTISNLPQ
FT INNE"
FT gene complement(18565..18810)
FT /gene="psaC"
FT /locus_tag=""
FT CDS complement(18565..18810)
FT /codon_start=1
FT /transl_table=11
FT /gene="psaC"
FT /locus_tag=""
FT /product=photosystem I subunit VII
FT /inference="similar to DNA sequence:NC_022409:CEXI_CP_p076"
FT /translation="MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRT
FT EDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY"
FT gene 53817..55307
FT /gene="rpl2"
FT /locus_tag=""
FT CDS join(53817..54201,54868..55307)
FT /codon_start=1
FT /transl_table=11
FT /gene="rpl2"
FT /locus_tag=""
FT /product=ribosomal protein L2
FT /inference="similar to DNA sequence:AC_000188:LyesCp030"
FT /translation="MAIHLYKTSTPSTRNGTVDSQVKSNPRNNLIYGQRRCGKGRNARG
FT IITARHRGGGHKRLYRKIDFRRNEKDIYGRIVTIEYDPNRNAYICLIHYGDGEKRYILH
FT PRGAIIGDTIVSGTEVPIKMGNALPSTDMPLGTAIHNIEITLGKGGQLARAAGAVAKLI
FT AKEGKSATLKLPSGEVRLISKNCSATVGQVGNVGVNQKSLGRAGSKRWLGKRPVVRGVV
FT MNPVDHPHGGGEGRAPIGRKKPTTPWGYPALGRRSRKRNKYSDNLILRRRSK"
FT exon 53817..54201
FT /gene="rpl2"
FT /locus_tag=""
FT /number=1
FT exon 54868..55307
FT /gene="rpl2"
FT /locus_tag=""
FT /number=2
FT gene 53517..53798
FT /gene="rpl23"
FT /locus_tag=""
FT CDS 53517..53798
FT /codon_start=1
FT /transl_table=11
FT /gene="rpl23"
FT /locus_tag=""
FT /product=ribosomal protein L23
FT /inference="similar to DNA sequence:AC_000188:LyesCp026"
FT /translation="MDGIKYAVFTDKSIRLLGKNQYTSNVESGSTRTEIKHWVELFFGV
FT KVIAMNSHRLPGKSRRMGPIMGHTMHYRRMIITLQPGYSIPPLRKKRT"
FT gene 14505..14672
FT /gene="rpl32"
FT /locus_tag=""
FT CDS 14505..14672
FT /codon_start=1
FT /transl_table=11
FT /gene="rpl32"
FT /locus_tag=""
FT /product=ribosomal protein L32
FT /inference="similar to DNA sequence:AC_000188:LyesCp036"
FT /translation="MAVPKKRTSTSKKRIRKNIWKRKGYWVALKAFSLAKSLSTGNSKS
FT FFVRQTKINK"
FT gene complement(24633..24896)
FT /gene="rps15"
FT /locus_tag=""
FT CDS complement(24633..24896)
FT /codon_start=1
FT /transl_table=11
FT /gene="rps15"
FT /locus_tag=""
FT /product=ribosomal protein S15
FT /inference="similar to DNA sequence:AC_000188:LyesCp029"
FT /translation="MVKNSVISVISQEEKKGSVEFQVFNFTNKIRRLTSHLELHKKDYL
FT SQRGLKKILGKRQRLLAYLAKKNRVRYKELINRLDIRETKTR"
FT gene 42157..42624
FT /gene="rps7"
FT /locus_tag=""
FT CDS 42157..42624
FT /codon_start=1
FT /transl_table=11
FT /gene="rps7"
FT /locus_tag=""
FT /product=ribosomal protein S7
FT /inference="similar to DNA sequence:AC_000188:LyesCp008"
FT /translation="MSRRGTAEKKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYR
FT AVKKIQQKTETNPLSVLRQAIRGVTPDITVKARRVGGSTHQVPIEIGSTQGKALAIRWL
FT LAASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRAFAHFR"
FT gene complement(25298..30973)
FT /gene="ycf1"
FT /locus_tag=""
FT CDS complement(25298..30973)
FT /codon_start=1
FT /transl_table=11
FT /gene="ycf1"
FT /locus_tag=""
FT /product=hypothetical chloroplast RF1
FT /inference="similar to DNA sequence:AC_000188:LyesCp019"
FT /translation="MIFQSFLLGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLL
FT RALVMEEGTEKKVSATTGFITGQLMMFISIYYAPLHLALGRPHTITVLALPYLLFHFFW
FT NNHKHFFDYGSTTRNSMRNLSIQCVFLNNLIFQLFNHFILPSSMLARLVNIYLFRCNNK
FT ILFVTSGFVGWLIGHILFMKWLGLVLVWIRQNHSIRSNKYIRSNKYLVLELRNSMARIF
FT SILLFITCVYYLGRIPSPILTKKLKEASKTEERVESEEERDVEIETASEMKGTKQEQEG
FT STEEDPYPSPSLFSEEGWDPDKIDETEEIRVNGKDKIKDKFHSHLTETGYNNINTSNSP
FT IYDYQDSYLNNNNTGNLENCKLQLLDKKNENQEQDLFWFQKPLVSLLFDYNRWNRPFRY
FT IKNNRFEQAVRTEMSQYFFDTCKSDGKQKISFTYPPSLSTFWKMIKRKIPLLSLQKTLP
FT NELDTQWVSTNKEKSNNLNKEFLNRLEILDKESLSLDILETRTRFCNDDTKKEYVPKMY
FT DPLLNGLYRGTIKKGVSSSIINNTLLENWEKRVRLNRIHTIFLPNIDYQEFEQKAYTID
FT KKPLSTEIDEFLTLINELGNEAKSSLNLKGLSLFSDQEQRRANSEKRTKFVKFVFNALD
FT PNETKSGKKSIGIKEISKKVPRWSHKLITELDQQMGEFKDRASMDHQLRSRKAKRVVIF
FT TDNKATKDAEEEVALISYSQQSDFRRGIITGSMRAQRRKTFISKLFQANVHSPLFVDRI
FT TPLRLFSFDISELIKPILKNWTDKEGEFKILESREEQTKREEKKEKDKKEDNKRKEQAR
FT IAIEEAWDTIPLAQIIRGYMLITQSILRKYILLPALIIAKNIGRMLFLQLPEWSEDLQE
FT WNREMQIKCTYNGVQLSETEFPKNWLRDGIQIKILFPFCLKPWHISKLYPSRRELMKKQ
FT KQKDDFCFLTVWGMEAELPFGSPRKRPSFFEPIFKELEKKIGKFKKKYFLTLKILKGKT
FT KLFRKVSKETTKLFIKSIGFLKKIKKELSKVNLIVLFRFKEISESNETKKEKDYLISNQ
FT IINESFRQIESGNWPNSSLIETKMKDLTNRTSTIKNKIERITKEKKKVTPEIDINPNKT
FT NNIKKFESPKKIFQILKSRNTRVIWKFHYFLKLFIQRLYINLFLSIINIPRITTQLFLK
FT STNKLIEKFISNNEINQEKINNKKKIHFMFISTIKKSLYNISKKNSHILCDLSYLSQAY
FT VFYKLSQTQVINFSKFRSVLQYNTTSCFLKTKIKDYFKTLGIFHSELKHKKLQSYRINQ
FT WKNWLRWHYQYDLSQIRWSRLMPKKWRTRVNQSCMAQNKNRNLNKWNSYEKDQLLHYKK
FT ENDSELYSLSNEKDNFKKCYGYGLLAYKSINYENKSDSFFSRLPFEVQVKKNLEISYNS
FT NTSKHNFVDMPGNLHINNYLRKGNILDRERNLDRKYFDWKIIHFSLRQKGDIEAWVKID
FT TNSNPNTKIGINNYQIIDKIEKKGVFYLTTHQNPEKTQKNSKKFFFDWMGMNEKIFNRP
FT ILNLEFWFFPEFVLLYNVYKIKPWIIPSKFLLFNLNTNKNVSQNKNQNFFLPSNKKIKI
FT KNRSQEAKEPPSQRERGSDIENKGNLSPVFSKHQTDLEKDYVESDTKKGKNKKQYKSNT
FT EAELDLFLKRYLLFQLRWNGALNQRMFENIKVYCLLLRLINPTKITISSIQRREMSLDI
FT MLIQANLPLTDLMKKGVLIIEPIRLSVKDNGQFIMYQTIGISLIHKSKHQTNQRYREQR
FT YVDKKNFDEFILQPQTQRINTEKTHFGLLVPENILWSRRRRELRIRSFFNSWNWNVVDR
FT NSVFCNETNVKNWSQFLGERKPLYKDKNELIKFKFFFWPNYRLEDLACMNRYWFDTNNG
FT SRFSILRIHMYPRLKIN"
FT gene complement(46313..53149)
FT /gene="ycf2"
FT /locus_tag=""
FT CDS complement(46313..53149)
FT /codon_start=1
FT /transl_table=11
FT /gene="ycf2"
FT /locus_tag=""
FT /product=Ycf2
FT /inference="similar to DNA sequence:AC_000188:LyesCp004"
FT /translation="MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFH
FT QERFLKLFDPRIWSILLSRNSQGSPSNRYFTIKGVILFVVAVLIYRINNRNMVERKNLY
FT LIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKISESCFLNPKESTWVL
FT PITKKCSMPESNWGSRWWRNWIGKKRDSSCKISNETVAGIEILFKEKDLKYLEFLFVYY
FT MDDPIRKDHDWELFDRLSLRKSRNRINLNSGPLFEILVKHWISYLMSAFREKIPIEVEG
FT FFKQQGAGSTIQSNDIEHVSHLFSRNKWAISLQNCAQFHMWQFRQDLFVSWGKNPPESD
FT FLRNVSRENWIWLDNVWLVNKDRFFSKVQNVSSNIQYDSTRSSFVQVTDSSQLKGSSDQ
FT SRDHLDSISNEDSEYHTLINQREIQQRKERSILWDPSFLQTERKEIESGRFPKCLSGYS
FT SMSRLFTEREKQMINHLFPEEIEEFLGNPTRSVRSFFSDRWSELHLGSNPTERSTRDQK
FT LLKKQQDLSFVPSRRSEKKEMVNIFKIITYLQNTVSIHPISSDPGCDMVPKDEPDMDSS
FT NKISFLNKNPFFDLFHLFHDRNRGGYTLHYDFASEERFQEMADLFTLSITEPDLVYHKG
FT FAFSIDSCGLDQKQFLNEARDESKKKSLLVLPPIFYEENESFSRRIRKKWVRISCGNDL
FT EDPKPKIVVFASNNIMEAVTQYRLIRNLIQIQYSTYGYIRNVLNRFFLMNRSDRNFEYG
FT IQRDQIGKDTLNHRTIMKYTINQYLSNLKKSQKKWFEPLILISRTERSMNRDPDAYRYK
FT WSNGSKSFQEHLEQSVSKQKSRFQVVFDRLRINQYSIDWSEVIDKKDLSKSLRFFLSKS
FT LLFLSKLLLFLSNSLPFFCVSFGNIPIHRSEIYIYEELKGPNDQLCNQLLESIGLQIVH
FT LKKLKPFLLDDHDTSQKSKFLINGGTISPFLFNKIPKWMIDSFHTRNNRRKSFDNPDSY
FT FSMIFHDQDNWLNPVKPFHRSSLISSFYKANRLRFLNNPHHFCFYWNTRFPFSVEKARI
FT NNSDFTYGQFLNILFIRNKIFSLCVGKKKHAFWGRDTISPIESQVSNIFIPNDFPQSGD
FT ETYNLYKSFHFPSRSDPFVRRAIYSIADISGTPLTEGQIVNFERTYCQPLSDMNLSDSE
FT GKNLHQYLNFNSNMGLIHTPCSEKDLSSEKRKKWSLCLKKCVEKGQTYRTFQRDSAFST
FT LSKWNLFQTYMPWFLTSTGYKYLNLIFLDTFSDLLPILSSSQKFVSIFPDIMHGSGISW
FT RILQKKLCLPQWNLISEISSKCLHNLLLSEEMIHRNNESPLISTHLRSPNAREFLYSIL
FT FLLLVAGYLVRTHLLFVSRASSELQTEFERVKSLMTPSSMIELRKLLDRYPTSEPNSFW
FT LKNLFLVALEQLGDSLEEIRGSASGGNMLGPAYGVKSIRSKKKDWNINLIEIIDLIPNP
FT INRITFSRNTRHLSHTSKEIYSLIRKRKNVNGDWIDEKIESWVANSDSIDDEEREFLVQ
FT FSTLTTENRIDQILLSLTHSDHLSKNDSGYQMIEQPGAIYLRYLVDIHKKHLMNYEFNP
FT SCLAERRIFLAHYQTITYSQTSCGENSFHFPSHGKPFSLRLALSPSRGILVIGSIGTGR
FT SYLVKYLATNSYVPFITVFLNKFLDNKSKGFLLDEIDIDDSDDIDDSDNLDASDDIDRD
FT LDTELELLTRMNGLTVDMMPEIDRFYITLQFELAKAMSPCIIWIPNIHDLDVNESNDLS
FT LGLLVNHLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKH
FT FFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVALTNEVLSISITQKKSIIDTNTIR
FT SALHRQTWDLRSQVRSVQDHGILFYQIGRAVAQNVLLSNCPIDPISIYMKKKSCNEGDS
FT YLYKWYFELGTSMKRLTILLYLLSCSAGSVAQDLWSLSVPDEKNGITSYGLVENDSDLV
FT HGLLEVEGALVGSSRTEKDCSQFDNDRVTLLLRPEPRNPLDMMQKGSWSILDQRFLYEK
FT YESEFEEGEGEGALDPQEDLFNHIVWAPRIWRPWGFLFDCIERPNELGFPYWSRSFRGK
FT RIIYDEEDELQENDSGFLQSGTMQYQTRDRSQGLFRISQFIWDPADPLFFLFKDQPPGS
FT VFSHRELFADEEMSKGLLTSQTDPPTSLYKRWFIKNTQEKHFELLINRQRWLRTNSSLS
FT NGSFRSNTLSESYQYLSNLFLSNGTLLDQMPKTLLRKRWLFPDEMKIGFM"

17
detectors/go_test.sh Executable file
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#!/bin/csh -f
#
set dirs = ("normalize" "ir" "rrna" "trna" "cds")
echo -n "" > test.log
@ nerr = 0
foreach d ($dirs)
(cd $d/test && go_test.sh) |& tee -a test.log |& egrep '^\+|\*'
@ nerr += $status
end
exit $nerr

18
detectors/ir/test/go_test.sh Executable file
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#!/bin/csh -f
echo "+ [testing IR]"
../bin/go_ir.sh test.fst > test.bak
diff -q test.bak test.ref >& /dev/null
set stat = $status
if ($stat == 0) then
echo '+ IR test Ok'
\rm -r test.bak
else
echo '+ IR test Failure'
endif
exit $stat

2593
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FT misc_feature 1..85882
FT /note="large single copy region (LSC)"
FT repeat_region 85883..111490
FT /rpt_type=INVERTED
FT /note="left inverted repeat B; IRB"
FT misc_feature 111491..129853
FT /note="small single copy region (SSC)"
FT repeat_region 129854..155461
FT /rpt_type=INVERTED
FT /note="left inverted repeat A; IRA"

18
detectors/normalize/test/go_test.sh Executable file
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#!/bin/csh -f
echo "+ [testing Normalize]"
../bin/go_normalize.sh test.fst > test.bak
diff -q test.bak test.ref >& /dev/null
set stat = $status
if ($stat == 0) then
echo '+ Normalize test Ok'
\rm -r test.bak
else
echo '+ Normalize test Failure'
endif
exit $stat

2593
detectors/normalize/test/test.fst Normal file
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2593
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18
detectors/rrna/test/go_test.sh Executable file
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#!/bin/csh -f
echo "+ [testing rRNA]"
../bin/go_rrna.sh test.fst > test.bak
diff -q test.bak test.ref >& /dev/null
set stat = $status
if ($stat == 0) then
echo '+ rRNA test Ok'
\rm -r test.bak
else
echo '+ rRNA test Failure'
endif
exit $stat

1111
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detectors/rrna/test/test.ref Normal file
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FT rRNA 1969..3468
FT /gene="rrn16S"
FT /product="16S ribosomal RNA"
FT rRNA complement(37878..39377)
FT /gene="rrn16S"
FT /product="16S ribosomal RNA"
FT rRNA 5664..8473
FT /gene="rrn23S"
FT /product="23S ribosomal RNA"
FT rRNA complement(32873..35682)
FT /gene="rrn23S"
FT /product="23S ribosomal RNA"
FT rRNA 8575..8677
FT /gene="rrn4.5S"
FT /product="4.5S ribosomal RNA"
FT rRNA complement(32669..32771)
FT /gene="rrn4.5S"
FT /product="4.5S ribosomal RNA"
FT rRNA 8934..9054
FT /gene="rrn5S"
FT /product="5S ribosomal RNA"
FT rRNA complement(32292..32412)
FT /gene="rrn5S"
FT /product="5S ribosomal RNA"

18
detectors/trna/test/go_test.sh Executable file
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#!/bin/csh -f
echo "+ [testing tRNA]"
../bin/go_trna.sh test.fst > test.bak
diff -q test.bak test.ref >& /dev/null
set stat = $status
if ($stat == 0) then
echo '+ tRNA test Ok'
\rm -r test.bak
else
echo '+ tRNA test Failure'
endif
exit $stat

1111
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FT tRNA 1670..1741
FT /gene="trnV"
FT /anticodon="GAC"
FT /product="tRNA-Val(GAC)"
FT tRNA join(3769..3767,3802..4562)
FT /gene="trnE"
FT /anticodon="UUC"
FT /product="tRNA-Glu(UUC)"
FT tRNA join(4627..4625,4665..5510)
FT /gene="trnA"
FT /anticodon="UGC"
FT /product="tRNA-Ala(UGC)"
FT tRNA 9317..9391
FT /gene="trnR"
FT /anticodon="ACG"
FT /product="tRNA-Arg(ACG)"
FT tRNA complement(9972..10045)
FT /gene="trnN"
FT /anticodon="GUU"
FT /product="tRNA-Asn(GUU)"
FT tRNA 15583..15662
FT /gene="trnL"
FT /anticodon="UAG"
FT /product="tRNA-Leu(UAG)"
FT tRNA 31301..31374
FT /gene="trnN"
FT /anticodon="GUU"
FT /product="tRNA-Asn(GUU)"
FT tRNA complement(31955..32029)
FT /gene="trnR"
FT /anticodon="ACG"
FT /product="tRNA-Arg(ACG)"
FT tRNA complement(join(35836..35834,35874..36719))
FT /gene="trnA"
FT /anticodon="UGC"
FT /product="tRNA-Ala(UGC)"
FT tRNA complement(join(36784..36782,36817..37577))
FT /gene="trnE"
FT /anticodon="UUC"
FT /product="tRNA-Glu(UUC)"
FT tRNA complement(39605..39676)
FT /gene="trnV"
FT /anticodon="GAC"
FT /product="tRNA-Val(GAC)"
FT tRNA 45660..45742
FT /gene="trnL"
FT /anticodon="CAA"
FT /product="tRNA-Leu(CAA)"
FT tRNA 53278..53352
FT /gene="trnI"
FT /anticodon="CAU"
FT /product="tRNA-Ile(CAU)"